Both of you should have checkouts of trunk and any branches you're both working on. When he is ready to have his branch merged into trunk, you should:
- Ensure that his branch builds successfully.
- Ensure that your trunk checkout is pristine (no SVN added, modified, deleted, unversioned or ignored files).
- Conduct the merge, resolving any conflicts with his help.
- Perform a code review, including ensuring that trunk is stable with his changes.
- Commit the merge.
Conduct the merge outside of Eclipse, using the SVN command-line. I've seen enough questions here on SO related to Eclipse and Subclipse that tells me the plugin is unreliable.
If it was me managing this workflow, I'd have two checkouts of trunk: one which is meant for merging and is always in a pristine condition, and another in which I can actively develop. That way, I wouldn't need to create a patch of my changes, then merge, then apply the patch.
Hope this helps.