Heh, it's nothing sophisticated, I just go to the position that is interesting on the game, and type my analysis manually on the comment box (Commands > show comments).
There you can type anything you want, so each information is easily accessible in any position. You can type there what are the game plans from that position, and if you have a big tree, often the opponent will transpose to old analysis and you'll have a well traced plan even if the opponent plays a surprising move (Commands > Add moves that transpose).
You can also type in each position the evaluation of different engines (like "Rybka 4 says the position is 0.13"), what I use is text of different colors, say, open WordPad and type "13", paint it red and copy it to a Bookup Comment box, then when you see a red 13 you know what it means, and you can use different colors for each engine.
You can type what the same engine thinks about different moves too, just write the move before the eval number (as in e4 13), and you can put different colored numbers after the same move to quickly see what other engines say about the same move, holes will be evident (like, if there's no red number after a move, you know you haven't analyzed that move with Rybka 4).
You can update those eval scores by rewriting them and propagate them backwards, to previous positions, say, if you can't find alternative moves that go beyond 0.13, you propagate it back to the root. As you continue evaluating positions Bookup will tell you how many variations you've analyzed (a number at the right of the move in the interface), that way you can check what moves have few variations analyzed and require more attention.
You can right click to delete moves from the tree (only the link is deleted, all the analysis and comments remain there), or color them (you've got no color, red, yellow, green, red+yellow, red+green, green+yellow and r+y+g), as for what you'd use colors for depends on the situation, I've been using green for "book moves", red for "risky moves", yellow for "human moves" (moves that I force myself that seem initially better than what the engine suggested and need more attention), but they can have many uses; or you can give signs to the moves, I use "!!" for "play this move immediately as it's clearly best", or "!?" for "move looked good at first, and then became risky", etc.
And finally, the best moves can be sorted at the top, this can be done by number of variations analyzed, or by assessments, that you give by clicking on the drop down box at the end of the variation and setting it (+/-, =, -/+, etc.) and Bookup will auto-sort the moves that are worse for this side at the bottom.
ALL my analysis methods take advantage of Book up, though I think it's an obsolete program superseded by Chess Opening Wizard, or something, but I tried a COW Beta and disliked it for some reason.
Anyway, good luck with Bookup! After what I've said, I think it's clear that the less interaction one has with the position, the less useful Bookup becomes, it may not be for everybody.