that is the easiest option...however you can get an adapter for 6.5" components for optimal sound quality...if you have money, thats what i would recommend because 6x9's are generally good if you don't have subs...
yes...6x9's are usually put in cars to give that extra low end (more surface area than 6.5" speakers)...but if you have a sub already...it would improve your SQ a lot to use the adapter to change it over...beware though...6.5" components cost more money...especially good ones...thats why i'd only recommend if you can spend a couple hundred.
no you will still hear them unless you have ungodly bass...in that case, you would need to add an extra pair of speakers anyway...your speakers will fire into the cabin and frequencies over 250 hz are directional so you will still hear it clearly...especially the midrange since that's what really carries the beat in music (not bass).