[fjtorres]

Installing extra apps is just a matter of copying the apk files to a directory of your choice on the internal memory or sd card and activating it using the Root Explorer file manager.
Getting the apks is not terribly hard; several market apps work fine.
Or if you have an android phone, several backup apps will let you copy out the apk.

Accessing books isn't a big issue even with the default Sony homescreen; the included Bar shortcuts app lets you tap the bar to call up a list of apps to run (among other things) and the reading apps themselves have their own book listings and you can tell most apps where to look for books.
Since both the default Sony and Alternate Home apps are only for epubs, other formats like Kindle books will be invisible to them anyway.
The way I use mine is to chose the reading app first and then go pick the book.
Resuming an open book just takes you back to where you left off.

Not much to be concerned about, really.
Standard android tablet operating rules.