I would recommend you to build up a nice directory tree for your project like one in Doom 3 ( see it on github - game sources and engine are lying near, but separately ).
And use one private repo.
Also making a .dll from your engine is a good idea to keep things clean.
I'm using this scheme and it allows me to keep all things close enought but not mixed together. I think that you will feel the need to change some code in your 'engine' part periodically ;) And you will have all by your hands to do it quickly.
GIT is a great tool