Yes, I understand what you mean. Make sure you have "Archive document in your Kindle library" checked in the Send to Kindle app.
Then you can download your docs from the Manage Your Kindle
page on your Amazon account. Everything you upload will be listed there. You can even restrict the view to Personal Documents
I don't know if you are using Calibre
, but it's great for storing and cataloging ebooks on your Mac so you can locate them easily.