chair flying in general is great for getting procedures down in your head. I also agree though in sitting in the airplane, when going through multi-engine procedures it really helped w/ the flow checks ... but make sure you make the noises, or else it won't be realistic, lol.
with a simulator, i believe they're great for getting you in procedural habits, such as instrument scanning, instrument procedures and approaches, etc. As far as actually helping with VFR flying, its minimal. But, for your private you'll be required to have atleast 3 hrs of simulated instrument time (under the hood or foggles in the airplane). Getting good at keeping the dirty stuff down and the clean stuff up and developing a good instrument scan can be done w/ MS flightsim, and therefore could be beneficial to your private training.