I know I've read somewhere that you can use a relative path in the unit coding (ie "../UnitFolder/UnitFlic.flc") to save mod size but it doesn't work for me.

What do I do exacty? Quotes? Backslash? Frontslash?

Its backslash. ;)

So if you want to use say, BowmanAttack.wav then you should put:

..\Bowman\BowmanAttack.wav in your ini files. In fact, if you use C3MT (Civ3MultiTool) to copy units, only a new ini appear in the new folder with the lines pointing to the various files. The same goes for all the ini files of the units I created. Thats why most of my unit flc are below 500k (other than the bandit) :D