Use magit-ediff or 'e' on an unmerged item to resolve merge conflicts with ediff. Magit will set up an ediff with three buffers A, B and C. A and B are the original (conflicting) files, and C is the conflicted merge.

If you need to manage multiple projects within a single repository, you can use a subtree merge to handle all the references.

Typically, a subtree merge is used to contain a repository within a repository. The "subrepository" is stored in a folder of the main repository.

The best way to explain subtree merges is to show by example. We will:

Make an empty repository called test that represents our project
Merge another repository into it as a subtree called Spoon-Knife.
The test project will use that subproject as if it were part of the same repository.
Fetch updates from Spoon-Knife into our test project.