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I don't have a T68, but I do have a rooted simple touch, which is also an eink android tablet, and I do the same thing. As a general rule, switching between books on the one piece of software is slow and annoying, because you can't have two open at the same time like you would on a PC.
But having two pieces of software "open" to switch between works fine on Android. Long-press the home-button to switch windows if you don't have the later-android window switcher button -- sorry I don't konw which andoid version is on the T68. If the T68 doesn't have an obvious route for this, you can also install "button saviour" which gives you nice, easily hidden, android buttons down the side of your screen.
EBookDroid is a nice simple alternative pdf viewer, fast and stable. Not much in the way of annotations but should be fine for your "endnotes version".
Once you've got two pdf readers installed, when you open a book you'll get a choice what to open it with -- as long as you don't "set the default app". You want to just set no default and open with first one reader, then the other.
(If you do accidentally set a default, just install any other pdf reader, and it'll go back to giving you the choice. Even, I think, after you've uninstalled your new pdf reader again.)
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