...how do I save the parameters to the quad once I type them into the boxes?...
There's a save button in the lower right corner of the screen. As long as the cc3d is hooked up it sends them to it and stores them in it flash memory. A lot of settings don't actually take effect until the cc3d is power cycled so once you've done the final save unplug and replug it.
...do I just skip the expert mode? Thank you very much!...
By expert mode I'm guessing you mean the stabilization sub-tabs Basic, Advanced, Expert? They're all different ways of looking at the same parameters, just do the Basic one. The others allow finer granularity of some settings but you don't need that at this point.
...do I need to connect a battery to quad when upgrading?
Not while upgrading the firmware, the USB power is fine for that. As you run the setup wizards after the firmware upgrade they'll tell you when you need a battery hooked up.
Do upgrade and erase on the firmware tab not just upgrade. The upgrade without erase sometimes leaves settings that cause problems.
Ask all the questions you want, it's better to ask and not need the info than to not ask and need it.