windows maximize to full screen and bottom hides behind the panel

how about this:

Settings Manager -> Panel -> Display -> Uncheck "Don't reserve space on borders"

Easy fix in Xubuntu 12.04 (you didn't say which edition you're using):

Right-click on the panel, select Properties (make sure it's panel properties rather than one of the launchers or applets on the panel_), then click the Appearance tab. Opacity should be set to 100.

If panels are set to "vanish" when not mousing over them, then open windows will go right over the "invisible" panel. Use the settings screen to keep the panel visible.

In ubuntu, you can reserve space for your panels with xprop, using the _NET_WM_STRUT_PARTIAL property (the reserved space is called strut). The idea is to get the ID of your panel window with xwininfo, and feed it together with the desired coordinates into xprop -set. If this answer seems to work for you, you can check out my blogpost for a detailed how-to and more info on using xprop.