No offense to you or anything, but if you are this unsure about the project you need to take some classes or find someone else to do it. Swapping an engine is not for the faint of heart nor is it for someone that has absolutely no experience doing so. This is not to say it can't be done, but I would highly recommend that you look up your local community college or tech institute and take some basic mechanics courses at the VERY LEAST if you have no background in the automotive industry.
Don't feel bad that you may not know either, I sure as hell don't know enough yet to take something like that on. It really is a lot of work, no matter what the experienced guys tell you, it is complicated. They just have a lot background in engine building so it may be a cake walk for them.
I am in no way discouraging you here at all, instead I am encouraging you to research and learn as much as you can before playing around with your car. Knowledge is power and if you are this unsure about what is going on with your engine you don't have enough knowledge about engine building yet. I would suggest you take your time and be patient. Do some more research, take some classes, and do this swap right.
