Ancestry is an online service that houses both databases and family trees. Access to trees are free; as well as some limited databases Most databases are available through a subscription, which was around $13 a month the last time I renewed (that's paying annually).
Family Tree Maker is a stand-alone program that runs on both Windows and Mac.
You can buy Family Tree Maker at your friendly software store or online in the online Store at ancestry.com. Be aware that the various names for FTM (ie premier, etc) only have to do with stuff that is tossed into a bundle - including various packages of online subscriptions to ancestry databases for various periods. There is only one current version of FTM (ie there is no good-better-best levels of the program).
As for your specific problems, I don't have enough specifics to advise what to do; but if you buy FTM, you can download ancestry directly into FTM - you can also "sync" FTM and ancestry so that if either is changed, the other will change. However, this is relatively new and there are people who have had problems with it. I, for one, don't trust the "sync" feature, but I still use the traditional upload and download options.
I would think you might get your ancestry file into FTM and start from there.