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I am developing and maintaining a complicated system project plan that comes from 3 different groups. Each provided manual scheduled time with start and finish dates, but they are not sequenced.
I am wondering if I should change those manual scheduled tasks to auto schedule to make the plan more useful. However, I don't want to mess up with the dates those groups provided. How should I handle this to ensure the best use of MS Project?
By auto schedule I think you mean a schedule with links--predecessor/successor horizontal and vertical relationships. If so, the answer is an unequivocal yes. Without that, you would have to manually calculate your critical path as well as future finish variances (FV) and impacts as you progress, which is impossible for a complex schedule without an army of schedulers making daily calculations and analyses.
Furthermore, once you establish your dependencies, you will likely find that the hard coded dates may no longer be accurate, in that the dependent relationships may cause tasks to start and finish on later dates. That is an important thing to know now instead of being surprised later.
This is not really an option. You need to build the schedule properly or acknowledge that you are running a complex project without a schedule at all.
