The versions will be installed in different directories and will be largely independent. Some "global" items that will not be kept separate are things like Simulation OPC server for OPC Classic but nothing that should affect you.
The only thing that really matters are the QuickOPC assembly references in your project. Check the directories they point to. Normally they will point to the subdirectory of the Assemblies folder under a specific QuickOPC version. The newer version should use a different directory and therefore your project should still be pointing to the right (the old) assemblies. If you want to be absolutely sure, make a copy of these QuickOPC assemblies into a folder *inside* your project's structure, and then re-establish the references, pointing to that place. Your QuickOPC assemblies will then be more logically group with the project - and certainly, no newer QuickOPC installation will attempt to replace them.