Marty is giving you good advice here. I always say that the toughest job for the Updox people is explaining exactly what the program can do. There are many ways to use it, fitting many different workflows.
Yes, you can still fax out via other means besides Updox if you choose to (this may provide a cost savings, though is not likely to save time).
Updox will archive every fax if you want it to, but keep in mind that the great majority of them are sent some where (primarily to the EMR). In other words, there is little need to archive everything elsewhere in case you don't stick with Updox.
As Marty says, your doc need not go into Updox to sign forms; on the other hand, once she sees how easy it is, you probably won't be able to stop her.