Hi Bob
If you select a person you want to be the 'root' of the tree, then create a filter in FTM to include just this person's ancestors, you can then create a gedcom containing just the people in that filtered list, which you can then upload to Ancestry. I've done this in my tree and it's pretty straightforward, as follows:
1. Select your cousin's maternal grandmother (or his mother to include both his maternal and paternal ancestors) in the 'People' list your tree, click on the 'Filter' button (below the list of names).
2. In the window that appears, click on "Ancestors...". A number of options will be shown in a pop-up (e.g. whether to include spouses and descendants), select what you want, click OK, then the Ancestors list will be shown.
3. After checking it has selected the people you want (you can manually add or remove anyone from the list), click Apply. Then save the filtered list under some meaningful name (click Save... under the list).
4. Now go to Export... (under the FTM File menu) and select Output format as GEDCOM. Under 'Individuals to export' select the name of the filter you've just saved. You'll see the people listed again so you can check it's the right folk. Tickboxes allow you to select what info to include in the gedcom, e.g. Media files etc. (they're all ticked by default but you can untick any of them). Then click Export and save the .ged file wherever you like on your computer.
5. You can then upload the gedcom to Ancestry in the normal way (and set up synchronisation if you wish), and link it to your cousin's DNA test.
Hope this helps!
EDIT: I should have mentioned to set up sync you'd need to save this as a separate tree in FTM, but that's probably obvious!