the 3.5 inch speakers can still be used if you dont want to go the 6.5 kick pannel route, just buy something of quality. personally ive owned and blown out 2 sets of pioneers. decided to step up and buy some Polk audio 3.5's and Polk audio 6x9's for the rear (needed 4x10 to 6x9 adaptors) IMO: 4x10s are a waste of time and money, none of them are made by quality companies and they dont have enough surface area to cover your mid range.. this will help you out alot, but to get that crisp sound you deff need an amp to atleast push the rear speakers... A 10 inch subwoofer and amp (mono or 2 channel bridged) would sound very clean in a sealed box, wouldnt have too much BOOM from that combo but just enough bass to help out your sound stage. keep in mind when buying a subwoofer dont go cheap!!! i'd suggest looking at Sundown Audio, they are an amazing company based in the USA and will absoutly crush the competition and sound great while doing it... dont worry about crossovers until you know what you are doing, some speaker sets come with external passives crossovers(component sets) and deff avoid active crossovers, they can be a huge pain to set properly and unless you know about db octives and slopes then i'd avoid active personally. the polks i suggested have built in crossovers fyi. one thing i also did in my monte was splice some tweeters with built in crossovers into my front channel and mounted them on my sunvisor mounts..
a few things to take note on, AMPS: always buy amps that are CEA-2006 compliant, this means they produce the advertised RMS wattage (dont pay attention to max wattage, look at the RMS wattage) also make sure the sub(s) you buy are going to be able to wire up to the ohm load that the amp can accept. most amps are 2ohm stable but some 2 channels in bridged mode will only be 4ohm stable, pay attentiion to this or you WILL fry your gear.. hit me up if you need some more advice.