I have done many rough's in custom homes over the years and this is what I have come up with.
1. Walk through job with home owner,Contractor,and cabinet maker first.
2. Using a benchmark instead of the floor for heights is a must.(this assures perfect heights).
3. If it is a definite location then mount a box,leave slack everywhere posible.If your unsure then float the wire,leave pleanty of slack for relocation and draw an asbuilt for reference after sheetrock goes up.
4. do a walkthru just before sheetrock goes up(again).
5. make any final adjustments.
6. If your still off, then CHARGE-CHARGE-CHARGE...$$$
