Where is our ability to add custom content
 

Still no way to add in custom themes Which is a problem with AP support so woefully behind. There are several APs that are out that we would love to run but can not add in custom content.

Example Fly Free or Die adds 2 new themes that we simply cant add in.

you can generally fake it with Permanent Adjustments.

Permanent Adjustments are a lifesaver. Also, for some things I added options with low, or easily ignored impacts to take up the "slot". For example, my dwarf mystic is actually a spell sergeant, but I took the "Battle Leader" archetype to make the appropriate trades because you can choose whether or not it impacts levels 4, 6, 9, and 18, and its abilities are easy to ignore.

Obviously not perfect, but there are tricks to use to get close to what you need.

So ... new theme Vaster from Fly Free or Die... Engineering is a class skill for you, if you already have Engineering as a class skill then add +1 to your Engineering. I have figured how to make it a class skill by using the override class skill in the adjustments. But I can not find where to add a +1 to skills. not can I figure out how to change theme knowledge .. any ideas?

Modifiers>Adjustments>Permanent Adjustments>Skill Points lets you add an extra skill point, just put the point into Engineering.

Theme Knowledge doesn't actually change any of your stats, just lowers the DC for certain knowledge checks. But if you want it noted on the sheet somewhere so you don't forget about it, you could make a custom feat for it (from the Feats menu) and type the description into the "Notes" text box.