If I apply for a fee waiver seat in aktu and the 5% fee waiver seats get occupied then will I be treated as a general candidate or I will be out of counselling?

Fee Waiver or FW seats are different from regular ones. You will have to give higher priority to seats with the FW option to opt for it. 

The simple procedure to apply for TFW seats is as follows:

1. The initial pages of the counseling form show the option ‘Will you opt for TFW seats?’. Tick it.

2. Now you need to fill in the choices that prioritize TFW mentioned options.

This part is a bit tricky so I have used an example to make you understand better-

If you want CS>>EC in IET>>BIET>>KNIT then your choice should be filled in this manner:

1. IET- CS(FW)

2. BIET- CS (FW)

3. KNIT- CS(FW)

4. IET- EC(FW)

5. BIET- EC(FW)

6. KNIT- EC(FW)

7. IET- CS

8. BIET- CS

9. KNIT- CS

10. IET- EC

11. BIET- EC

12. KNIT- EC.

Placing your priorities in this manner will surely get you a fee-waiver seat.