Could you explain in a little more detail what you're doing? I can't quite follow what the issue is.
I am having the same issue as maxwellreed, and haven't been able to find a solution. When I drag graphics from my CC Libraries to my AE project at work, a file is created locally on my computer. When I open the project on my home computer, all files are missing, since they are saved locally on my other computer. Is there a way to force AE to save them to my Creative Cloud instead, so I don't need to go through the process of dragging all the graphics in to the project again?
When you add an asset from the Libraries panel to a project in After Effects, a copy of that file is made locally (in your User folder), and that is the file that the project references. It is no longer associated with the original asset in your Creative Cloud library.
This was an intentional decision we (the After Effects team) made during our initial implementation of the Libraries panel in After Effects CC 2015 (13.5). This protects against an underlying mechanism of the library assets, which are stored under directories assigned unique GUID codes (ex. "0a6e7a74-18f4-4cd2-984d-da5b813ac262"). If a Library asset is updated, renamed, or otherwise changed, that GUID code can be changed without After Effects being notified, thus causing the asset to go offline. We decided that was bad, your files shouldn't go offline.
In other words: we made a choice between disconnecting the file from the source library asset so that it doesn't update or having the asset go offline if it was updated.
Since that initial implementation, Libraries now has a concept of "linked assets", a mechanism that automatically updates instances of the library assets where they are used in a document or project. This is available now in Photoshop CC 2015. We plan to add this capability to After Effects in a future update.