Well yeah you have to plug all the power cords back in. However, that isn't that difficult, just remember what kind of plug was plugged in where. And the problem with running a system off of a power supply that does not have ample 12V rails, it may not power the system correctly or could even blow and take some of your components with it.
Yep you will have to do that. Take note where each cable is (make a drawing if necessary) before unplugging things.
Besides... you won't be able to plug most connectors unless you're doing it the right way.
Just don't force it.
If you feel you're really forcing it then it means you're most probably plugging it the wrong way or not all pins are aligned (on an IDE cable for example). Take your time when doing it.
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