in the FPE for your entities, try altering the offset,
example below is the stock AT gun FPE , changing the offx, offy, offz will move the entity object's position in these planes. Once you change the entities offest, delete the associated Bin file and reload it into the editor.
Like others, I have come to hate those *(*&%^^%^# BIN files!!!
;header
desc = artillery_gun
;ai
aiinit = appear1.fpi
aimain = default.fpi
aidestroy = disappear1.fpi
;spawn
spawnmax = 0
spawndelay = 0
spawnqty = 0
;orientation
model = meshbank\ww2\scenery\special\artillery_gun\artillery_gun.x
offx = 0
offy = 0
offz = 0
rotx = 0
roty = 0
rotz = 0
scale =100
defaultstatic = 1
materialindex = 0
collisionmode = 1
;visualinfo
textured = texturebank\ww2\scenery\special\artillery_gun\artillery_gun_d2.tga
effect = effectbank\bump\bump.fx
castshadow = 0
Uhu Berserker
Warfare Unlimited R&D