firstly this is a car tech forum not ice
but ill have a go anyway
1) you say that the front speakers are underpowered if you leave the inline amps in??
confusing that one please rephrase
also are you sure that they are inline amps my thinking is that they are crossovers used to split the frequencies to the seperate drivers
but if they are crossovers you will not need to remove them check for a live feed to them and a grounding point to check if they are amps.
2) yes if your into your lows and really want to feel the music then yes you should
but if not then your bose drivers should producre sufficent bass for your needs.
an amp would naturally be kept close to the sub for becsue subs are usually kept is the boot for i. more space and ii. subs produce lower frequencies that can not be defined from a certan angle they have no imageing.
3) go to your dealer and ask them there they will direct you how
otherwise i don't have a clue!