As far as what you need to do regarding syncing up your two web providers you now have your mission.
One more point about GEDCOM. A person record always starts with a 0. So in the case of your "Ebenezer Snell" the first line you should capture for your data send to RootsWeb should be:
0 @P41044@ INDI
Copy in the GEDCOM file down to the next person, which will start with another 0 in the first position of a line in the file.
Regarding your move to webtrees. First the website is
www.webtrees.net. This software will require you to learn a lot more about computers to use. It may not be right for you. If I was in your shoes, with your background in computers, I would drop one of your website providers completely. Unless the two companies can provide a bridge so you can copy your data from one to the other easily, having these two sites will continue to be a pain.
Moving to webtrees is a great option but you have a lot to learn. You will need to know how to copy pictures and documents found on the Internet to your hard drive and then up to your new website. Data entry and citations will not be point and click like on ACOM. The upside will be that your data on webtrees will be more open, better organized, and controlled by you.