u mean underbody tray or the rear diffuser itself??...
underbody tray, u diy some sort of opening for easy access to oil sump and oil filter lor...
as for exhaust pipe... dont weld dead ur underbody tray lah... use bolts to secure it in place... when u wanna change exhaust piping, jz remove the bolts to remove the undertray can adi...
as for ur rear diffuser, best is to cut the shape according to ur muffler.... something like this...
jz make sure u aint planning to change ur muffler in a vr long time... or else u might have to diy another rear diffuser and cut it into shape again... haha...
as for ur 2nd question... if u dont cover up the whole undercarridge also can la... less effective lor... jz cover those huge gaps such as are between ur front bumper and under ur radiator.... and the exit jz before ur rear bumper (where ur rear diffuser will be)....
do more research on how car underbody aerodynamic stability works... good luck...