I rarely use Dynamic Link, but it sounds like it works like an Illustrator or Photoshop document imported into AE.
If you import either kind of document into AE, you can animate the layers. But if you decide later to add a layer to the document, you won't find the new layer in your AE project. You have to import another instance of the document into AE, then mess around with replacing old layers with new ones, eventually adding the new layer to the AE comp.
Not sure what you are saying. If there is no comp in the project window (or "bin area" in your words), it doesn't exist - short of perhaps having hidden in one of the folders there. Clarify what exactly you are doing. Also screenshots of your respecive windows and import dialogs might help (attach them using the camera icon). And finally, do provide some system info, what footage types you use, comp settings, sequence settings in Premiere and so on. The weirdest things can influence this stuff from some bad comp naming to hard technical issues anything is possible.