You will have to mark all facts that you don't want to upload as private. This can be done by using Edit>Manage Facts>Data Options, IIRC. The Export to GEDCOM allows you to ignore private facts and notes.
I would make a copy of your tree before doing this.
Then, instead of creating the GEDCOM you should look into using Share (click on the little green Ancestry Symbol up in the right hand corner of the Plan workspace) which will upload to Ancestry directly without going through a GEDCOM.