I think you are going about this the wrong way. At this point you have two trees, the one you created in FTM and the one you created over two weeks on Ancestry.com. Uploading your FTM tree to Ancestry and merging them on Ancestry will not solve your problem of having two different trees.
I would download your Ancestry tree to FTM as a new tree. Do not use the sync feature when you do this. After backing up both your current FTM tree and the one you downloaded from Ancestry you can carefully merge the smaller Ancestry tree into your FTM tree. Once this is done you can delete both trees on Ancestry and upload the merged FTM tree to Ancestry using the sync option. This will allow you to have updates to one tree copied to the other.