Bemko: The best way would be to to put a Male header on J7 and a Female header on J3. Break the Programmer section from the main board. That way you could unplug the Programmer section from the main board and then you would be assured that the USB ports would not interfere with each other.
AFAIK it is not a problem to have both connected at the same time.
As hli said you can keep both USB port connected in parallel. The related 5V supply lines are connected together (via diodes D1,D2,D7,D8) into the power supply unit. All board voltages are generated from there.
Looking on the schematics (Kit Guide Page 40...) there is a remark to update firmware for "USB backvoltage compliance" (Page 42 Fx2LP Programmer section)
All the Best