I assume you have already created the paletes. After that , add a line to the .def file with the name of the pallete;. If you named the pallet pal1.act add pal1.act on the def file as shown below: [Files]
sprite = wonder_reloaded.sff
anim = wonder_reloaded.air
sound = wonder_reloaded.snd
cns = states/wonder.cns
st = states/wonder.cns
stcommon= states/wondercommon.cns
pal1 = pal1.act
pal2 = pal2.act
pal3 = pal3.act
pal4 = pal5.act
pal5 = pal4.act