I have noticed that some people on here have requested some kind of integration og reference managers (ie EndNote) into Atlantis.
I myself uses Zotero (a free Firefox extension) as a reference manager and it works very well with Atlantis.
Just use CTRL+ALT+A in Zotero to copy a citation and then just paste it into Atlantis. Use CTRL+ALT+C for copying the full bibliography.
In this way you can still use Atlantis and add references in an easy way.
I hope it may be of help to some of you!!
.Max