The best way for clear and seperated sound is to go to component speakers where each speaker is seperate.
read about in the following link.
More on this subject is here.
If you don't have room to mount all of the different speakers or don't want to go thru all of the trouble then the choice is yours.
Just remember it is better to have speakers in your car, then to get in over your head with installing more then you are capable or wanting to. This usually ends up with a half finished job or having a stereo store finish it.
Sometimes a 6" will fit in the 6.5" but I wouldn't count on it. It depends on the actual hole size.
They do make adapter rings for some speakers/vehicles.
Here is a link to 6.5"speakers
There are also reviews on some of the speakers.
a 6.5"speaker will usually produce better bass but that depends on a lot of things. Speaker travel and how much power it can handle/ how much power is being sent to speaker etc.
One thing to remember is don't by a speaker that is rated for a 200watts and power it with 40. It doesn't produce very good results.
Hopefully this will help with your install. Good Luck.
Hope I didn't confuse you more.
You don't need everything that this site recommends. Budget/Best sound is the most important.