When I plan out enhancements for a build I typically move stuff around all the time. Ron's planner is an excellent utility and I do use it to validate my builds and post them to the forums, but for actually planning out enhancements I use a spreadsheet for the bulk of the work.
Let's look at my Pale Trapper enhancement list for the U19 enhancement pass for an example. I haven't verified that this loadout is fully compliant with AP gating yet; this is the rough draft. (I verify by simple visual inspection.)
The first thing I do is manually enter the name, tree, tier, AP cost and level for every enhancement in every available tree I might want. Note that the level I enter is an adjusted value that may be higher than normal due to splashing levels in another class, requiring a feat I don't take until higher level, etc... In this example, level 1 wizard enhancements aren't available until level 2 since I take a rogue level @ 1. You can also see the levels where I take the metamagic feats pretty clearly, since I "improve" them immediately.
After adding every enhancement I might want from all trees available I fill column G with TRUE for all of them. The running total at the top of column H shows me how many I've selected so I can see at a glance how much I need to prune.* Note that I keep the top row frozen so I can always see the running total. The formula for column H (included in the screenshot) is pretty straightforward, and the header for colum H is a simple =SUM(H2:H200). 200 is just an arbitrarily high value to ensure it catches them all.
Once all enhancements are added and flagged as TRUE I sort the list by Tree => Tier => Enhancement. Then I go through and starting deleting TRUEs to prune the list down to 80.
Once I'm down to an 80 I'm happy with, then it's time to verify if this is a valid list of 80 AP. For this I sort the sheet by Train => Tree => Tier and manually count the AP spent in each tier to make sure I meet "points in tree" prereqs. Once I have a valid set of 80 points worth of enhancements, it's time to order them.
Ordering them is my favorite part; I love intricate planning. First I reorder the sheet to Train => Order => Level, which is the final sort order. Each time I add a level or 2 worth of ordering I quickly re-sort. (For order notation, 3.2 means "second enhancement taken at level 3.") I typically choose a few key enhancements as "set in stone", taken as early as allowed. For this build the markers were the core enhancements, empower/maximize/quicken efficient metamagics, and I wanted 1 Int taken at levels 7, 8, 11, 12 and 20 to complement a previous-life +4 tome combined with levelups.
After the ordering is complete (and while setting the order) I use column I to verify that my order satisfies "points in tree" requirements. This used to be a much simpler affair for the old enhancement system with its "total AP spent" progression. For "points in tree" I had to write a macro to call, sending cell ranges to the macro. More info on column I's formula and implementation in the second post.
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*With only 86 AP chosen for wizard it was not hard at all to prune the list down to 80. For my other builds it's usually between 100 - 130 AP total.