Would it be wise to buy this pre-built system then upgrade it?

Can't see your links, but maybe consider a barebones kit instead. You could buy and upgrade, but keep in mind you probably void the warranty, and also you will likely not be able to upgrade your processor later. Many times too the boards in prebuilts are not impressive, to me anyway.

Once I picked parts though, last build I did I only had a little over an hour assembly time. Do this. Check and see if you've got a microcenter around. Many times they will have combo deals where if you buy an AMD processor, you get a board for nothing or nearly nothing. Many times the guys there can help you pick your parts, and they are pretty comparable to newegg price wise, and will sometimes match newegg pricing. Go in there, talk to those guys, tell them what budget you have and what you want to do, they could probably recommend you the parts and get them all picked out, all you would have to do is take an hour or two to assemble and install OS. Plus, if you spend a little extra, many times you can do 2 year walk in warranties on the parts, so if you have problems deal directly with them.