The parameters to edit an aircraft's radar and IR signatures can only modified in the .PT file. The .PT file is in your /Fighters Anthology/Toolkit/Project/Projectname folder, and will have the aircraft's filename that you have specified in the toolkit. Open the file with a text editor. Below is the text from inside a file. Scroll down and you'll see that I've marked the pertinent lines:

[brent's_relocatable_format]

;---------------- START OF OBJ_TYPE ----------------

;---------------- general info ----------------

byte 5
word 540
word 541
ptr ot_names
dword $12bf3
word $ffff8000
ptr shape
ptr shadowShape
dword 0
dword 0
word 30
word 0
word 0
dword 0
dword 0
word 0
word 20
word -30
dword 0
dword 1956 <<<<------ this is a good line marker, the service entry date
word 111
word 0
word 77 <<<<------ Visual signature
word 77 <<<<------ Laser signature
word 100 <<<<------ Infra-red Signature
word 100 <<<<------ Radar Signature
word 0
word 115
etc.

The lower the number, the smaller the signature. 100 is the default value. Try opening the B-2, F-117, and F-22 files (you'll have to save it in the project first, so the file shows up in the folder). You'll notice that the signatures are smaller than default.

Making the signature smaller does not make aircraft fully as stealthy as the B-2, F-117, and F-22, as these aircraft seem to have a built in stealthiness. This effect can only be replicated by basing a new aircraft on one of those three. However, editing the signature through the PT file can still have a major effect on aircraft and missiles in the game.