You can indeed. Just add another project in boinc manager.
You set the resource share of each project on the project's website (defaults to 100). So if you added say nQueens you would have both Aqua and nQueens at 100 each which gives a 50% share for each. Boinc would then download workunits from each project and it would handle running them equally.
Pretty much hands off. Best way is to try it and see what I mean though. A picture paints a thousand words and all that