Yup. I mounted the tweeter over the stock tweeter "hole"... came out very nicely. My main amp (front and rear speakers) is mounted under the drivers seat, and the amp for the sub is mounted behind the jack in the jack compartment.
The 6.25" Bostons should fit (in theory), but you want to check mounting depth to make sure they don't run into the window track. Also, you may have to do a little trimming on the stock speaker mount... but it should be much, if any.