There are a few threads on this subject.
I have the Alpine head unit in the glove box with a RF repeater and remote so I can tune and adjust volume with the glove box open or closed.

I bought another set of A-Pillar moldings and mounted tweeters up hi in them (no one ever notices them even at shows.
I have a dual speaker in the dash, 4x6 high end speakers in the stock kick panel locations under stock grills.

Vikki was able to mount slim line 6.5" speakers in the side panels where the top folds down

I have 6x9's mounted in boxes firing forward where the top folds down, a 4 channel amp and a sub in the trunk
I plan on doing better custom boxes for the 6x9's and a permanent enclosure for the sub (just a 10" Bazooka tube right now)

I must say I'm pleased with how clear it is top up or down. I actually have to have the tunes turned down if I have people in the car on the freeway, top up or down. But as I mentioned I'm still configuring everything in the trunk and will make custom panels to hide everything at some point...

So lots can be done with out being too invasive or doing anything that can't be undone...

Here are a few pix (Tried Bass Shakers under the front seats, but removed them)
Interior installation pix