Import is okay, by the way. You have the wonderful opportunity to review and qualify every component, and set a consistent design style. Complex and nice footprints can be saved. Poor ones can be corrected. Bad ones can be skipped.
Imports are always on weird layers, and bring a lot of fluff that you don't need. Like, Eagle imports might bring separate "cream" (paste) and component outline and body layers, and so on, along for the ride. Several of those you'll want to either delete (paste is automatically derived from the pads), reassign (component outline --> Mechanical 13), or clean up (avoid silkscreen on pads, use clean lines and arcs?). Some of this can be done en masse: with the Filter and Inspector panels, you can select objects in all footprints in the library and change them all at once.
Follow a naming convention. You can have separate library files for classes of components, drawn along whatever lines you like: manufacturer (AD's built in libraries do this), component type (passives, ICs, connectors..), or a monolithic, catch-all library.
Naming is the most notable change I've made, in my personal library, over the last, hmm, I've been using AD for 7 years I think? I had also gone through and made some graphical changes. I don't have such a large library that I can't remember all what's in it, but having parts and footprints categorized by purpose makes it much easier to find them. I used to name things by generic (e.g. "R0805" for SMT chip resistor) or part number ("CMS1" for a certain SMT choke), now I've added categories ("IND_CMS1", "CAPAE63X60", "SOIC-8", etc.).
Oh, and don't use underscores everywhere. Or ALLCAPS. It's terribly ugly. The 1990s are over. No one needs short file names, caps, space-free names, or anything like that. You are free to make your files smooth and presentable!
(Okay, a quirk in my system, I maintain ALL_CAPS and underscores in footprints. I think footprints are still one of the informational backwaters in the world, unfortunately. To be fair, ALLCAPS looks better in stroke font, and is still traditional on mechanical drawings. My component libraries are easier reading though, like "Ind FB 1206 390R 2A", which is short and descriptive.)
Tim