Suppose you have something like:
/prj/workspace/prj1
/prj/workspace/prj2
And your eclipse workspace is in /prj/workspace level (i.e. /prj/workspace/.metadata). If you're having problem importing prj1 and prj2, you can either move your .metadata somewhere else (/prj/.metadata, /prj/eclipse/.metadata, etc.) or create a sub level in workspace so that it looks like:
/prj/workspace/android/prj1
/prj/workspace/android/prj2
And import prj1 and prj2 again. In another word: as long as prj1, prj2, and .metadata are not in the same level it will be fine.