If I understand you well, You are currently running 6 different installations of WordPress on a single domain for different projects. The installations are at different directory levels. You are wondering if you can have multsite and have specific users access specific sites. The answer is all this is possible and you will end up saving lots of resources. But since WordPress has a dubious habit of depending on URLs to resources it needs you will have to do some database clean up as you are going to end up with a few dead links. If you would like, feel free to read : WordPress Multisite vs. Multiple Sites