Why was Thomas sent to the Glade?

"Thomas is part of the organization that created maze, then why was he sent to the Glade?"

According to this conversation, It is not stated in the movie why Thomas and Teresa is sent to the maze even though they worked as the part of organization.

-Why would they send us up if we were with them?

-It doesn't matter.

-He's right.

-It doesn't matter. Any of it.

But as per my understanding, sporadically you keep hearing that Thomas was one of the creators favorites and for years others were failed to complete the maze. So, they wanted to test whether Thomas can do it or not and he does that. And also in the end, Ava Paige says,

Thomas continues to surprise and impress.

So, it sounds like it's part of Ava's plan to send Thomas to the maze and manipulate others to complete Phase One.

"Once sent he had no previous memory like others then how is he to able witness flash backs of his past?"

It's not only Thomas had flashbacks but whoever is infected with the poison injected by the Griever.

"The purpose of whole research was to analyze potential of all boys or just Thomas?"

By the words of Ava Paige in the end, it should be to analyze potential of all boys including Thomas.

The purpose of whole research was to analyse potential of all boys or just Thomas?

The Purpose of the Maze and the other trials are to find a cure for the Flare, an infectious disease that causes madness and cannibalism (think Rage Zombies). A small percentage of the population is immune to the Flare, and the younger the more immune they are. All the Gladers were found to be immune prior to being sent to the Maze. The events of the Maze are set up to induce the Immune's brain in producing an enzyme which can be used as an injectable treatment to prevent or slow down the Flare in non-immunes. Note that the second movie events have diverged from the books very much. There are multiple Mazes and groups of gladers, numbering in the 50~100. Many more are seen being harvested for the enzyme.

Killzone is the part of the brain affected by the Flare. This name is adopted after the Flare starts infecting people. The disease slowly eats away the Killzone, turning the infected (known as Cranks) into madmen. WICKED tries to use the patterns in the Killzone of those immune to the Flare to develop a cure, so they send a number of immune "subjects" into the Trials to obtain these patterns.

The key part of the trials is that the Flare eats away at the brain faster when the brain works harder. The same is true for the Immunes. The harder they think, as in life-or-death split second thinking, the more of the immune enzyme is produced. The purpose of the whole research is essentially using human lab rats as a medicine factory. According to Ava (The head bitch in charge), the enzyme can not be synthetically reproduced. In the books, the brain needs to be checked, which requires the brain to be removed. _{Apparently they never developed MRIs in this reality.}

Once sent he had no previous memory like others then how is he to able witness flash backs of his past?

It hasn't been explained outright in either The Maze Runner or Scorch Trials movies. In the books, each Glader is microchipped with the Swipe. It allows WCKD to control their actions and wipe their memory. Based on the events of the first movie, it's likely that the flashbacks are WCKDs method of controlling the events of the Glade, and pushing them towards the exit. In the second movie, the Gladers are shown to have been chipped for identification at least, with Theresa being given her full memory back, with a scene implying that the chip was involved with that happening.

Why was [Thomas] sent to the Glade?

Thomas was sent to the glade because:

He betrayed Wicked to the Right Arm, a military group opposed to WCKD. The Right Arm is much smaller than before. Since he's immune to the Flare, they thought he'd be more useful in the Maze than dead.

Ok, now I have the full story because I have read all of the Maze Runner books. Thomas was sent to the Glade because of the following story:

Dr Ava Paige had slipped a note in under Teresa's door in the WICKED complex and it had read:

"Come see me immediately after receiving this note"

So she met with Thomas and they went when it was dark. Paige opened the door when they knocked on her room door and she let them inside.

She told them that there are 19 workers inside WICKED in the North wing as I am sure and she has asked Thomas, Teresa, Aris(who came just after Thomas and Teresa) and Rachel (who came with Aris) to kill the infected by a poson Paige had concocted herself and gave the four bags with the mixture in syringes, and they said "better too many than not enough", so Teresa went with a hand gun, both Aris and Rachel took Launchers and Thomas only had a back pack, and they went on the assassination mission.

When they got back and they returned to their normal activities and schedules for each and every day, but Chuck had come onto the scene and Thomas started to become fond of Chuck after finding him in a hallway sitting down crying at night. Thomas later on when his friends had their memories wiped and Thomas observed them in glade from the Observation Room but he later tells Teresa that Chuck has set him over the edge and he now disbelieves in a 'cure' for the flare.

He felt sorry for his friends in the Glade because Newt tried killing himself and he was furious because WICKED let a kid die in the Glade after being stung by a griever in broad daylight and resolves to rescue his friends from the maze. Thomas tells Teresa his idea and they go to the meeting called on by (by the way, Thomas and Teresa had built and programmed the maze optical illusions such as the sky and Griever hole) Ava Paige but Thomas is angry at her for using his email as a way of her becoming the Chancellor and she stated that it was effective immediately after the previous Chancellor had deceased.

So Thomas proposes his idea of the four of them being sent into the maze but keeps back the fact that he wants to rescue them, but he claims that they can pass information back from the glade into the Observation in real time and Ava is delighted with this idea, and she later approves it and Teresa and Ava come up with a plan while Thomas does as much research as possible for an advantage over the grievers.

When Thomas is on the day of going into the Glade, Ava gives him a special 'tea' made specially for him and says the SHE gave the workers the Flare because they wanted to stop experimenting after the Maze Trials but she didn't want to and poisoned them and killed them using the kids. But Thomas had been tricked and he passed out when drinkng the tea and he went for the swipe by force and without being able to do anything.

Sources: Read all of the books and you will know what I am saying.

It was my understanding that all boys were to be analyzed. In fact, the ending indicated that the entire end sequence where they finally escaped the maze and found the laboratory was a simulation, as the woman running the show was believed to have committed suicide and yet at the very end sat at a meeting table to discuss a second test for the boys.