A nice clean cut in a dash is fine.
And if you are running a sub, you need an amp for that. A small amp for the speakers will not hurt either. I have a deck that puts out 45 X 4 and it does okay, but just does not handle the bass real well at higher volumes.
I bought some prefab Truck speaker boxes for 6X9's. The way the boxes are setup, they actually fit where the 6X9 is facing upwards. This helps the muffle sound, but sometimes the highs could blow your ear drums out!