I'm using BOINC Manager 6.4.4 on linux and I have it synchorised to my gridrepublic account. I was looking at the BOINC website and I found a project I want to add (AQUA@home) but it is not on the gridrepublic list, if I add it through the BOINC Manager would it conflict with my gridrepublc account and stop working or cause some problem?
Adding the project manually will not cause any problems with how GridRepublic works with your computer.
The only difference is you will not be able to manage the preferences on GridRepublic.org for the project(s) that are added to the manager manually.
To change those prefernces you will have to visit the project's website.
*GridRepublic updates its project list periodically to support new projects. You may see AQUA@home in an update and would be able to add it on GridRepublic.org to manage it from GridRepublic.org without risk of losing credit.