So you have everybody in one FTM file, right?
Did you then go to the adopted person and
1) Main Menu in People Space > Persons > Attach/detach > Attach Father and attach the father (with the appropriate wife)?
2) Go to the Person tab of the adopted person's parents and click on the "relationship" button in upper right. Choose "adopted" status?
3) Staying with the "relationship" view, navigate to the adopted person via the mini-tree on the top of the page and enter which parents are preferred (usually the natural parents.)?
These actions will:
1) include the preferred parents in ancestral reports.
2) include the adopted person's descendants in the descending tree of either natural or adoptive parents.
That said, I would prefer to
Enter a Fact for Notes or whatever Fact you want and print in large capital letters "ADOPTED"
1) Run two ancestral reports. 1) One with the natural parents as preferred. Then 2) change the preferred option to the adopive parents and run a separate one for the adoptive person and his adoptive parents and ancestors only.
2) For descendant reports - the adopted person will appear in descendant reports. This is a bit misleading, FTM includes no information that this is an adopted branch of the family. I would prefer it if FTM had a text string somewhere in a Descendant Register report that this is an adopted branch. That's kind of hard to do with charts and the outline descendant report.
In the surname study I am currently doing, I am referring to the "ADOPTED" text string in a Note fact as the means to filter for a separate report of adopted persons into that surname. I consider the adopted people into my surname database a separate set of data, just as people that I have found that are not attached to my main surname trees are "unattached" and form another dataset.