the lighter the better, white is ideal, but being an ameratur (i know i cant spell) no metallics is better do to tiger striping, imo there is more room for error with a SOILD color, do you plan on base clear or single stage? if single stage DEFFINATLY a solid color.
ive been there with you on the filler question,depending on how bad it is, would be the best way to decide what to do, just Make sure there is a good moisture barrier behind it, thats key!
and if you know there will be flaws, advice, gett the car the way you like, the get a gallon of MAR HYDE 2k high build primer {like $75} (the thick yellow stuff) and be sure to reduce it like 10% (makes easier to sand) and over the hole car or just questionable areas do 2-3 nice wet coats, let dry and get a long hard block (dura blocks are very nice) and block the areas down by hand, in a criss cross action ///\\\, even cheap black spray paint as a guide coat, and it you do guide coat it just mist the paint over it.
hope this helps