This is all from my shoddy memory, but I think it covers most of it.
The middle panel with the armrest is only held on by one clip once the armrest screws/bolts are removed. The clip is towards the leading edge of the panel (towards the front of the car) a little lower than the armrest and back about an inch or so. Once it's loose, work the panel forward and down, as there are tabs which hold it in along the top and at the back. Disconnect the tweeter and you're done.
This will reveal the three bolts which hold the top piece in place. Make sure you remove the small plug holding the weatherstrip in place and starting from the front, pull the trim piece straight up. You'll need to release the arm that moves the retracting flap thing (no idea what you'd call it...) and that should give you full access to mounting the hardtop kit. There are a row of clips that hold the trim piece in place along the window, but it's pretty self explanatory once removed.
One piece of advice: do a trial fit of the hardtop with the kit installed, but not tightened, and before you put the panels back in. Good way to make sure the top is sitting right where it needs to before it's all buttoned up. There's not a whole lot of adjustment even possible on the mounting brackets, but the bolts are a lot easier to get to now.