Often times you can tell by watching an LED on D13, see what kind of link sequence it is doing.
You can design your board to not have an ICSP header, but just make a breakout cable to connect the programmer to the appropriate pins to program it. Make your design to not have D11-12-13 used as inputs (instead be outputs to other devices) to eliminate signal contention.
Or program the parts before mounting them on the board.