you can only have one tree linked to your DNA test(s) at any particular time.
That's disappointing. Ideally I would split my tree into two, the paternal and maternal lines as there is no crossover between the two.
I am not sure why you would want two distinct Trees.
Personally I would keep one tree and then in Software like Roots Magic I would sync the whole tree into a Roots Magic project, and then check for Problems, Duplicates and perform a Tree Count, these actions would clear any issues.
Then I would start a new Roots Magic Project, select Father in the whole tree and drag him into the new project.
Then do the same with the Mother.
I would add myself and set me as the home person, then upload both trees to Ancestry.
So now on Ancestry I would have the whole tree, a Paternal tree and a Maternal tree then I would swap over the DNA link to myself in each tree, keep it there for a while and swap over as often as required.
With a strong DNA match I build a tree in Ancestry around them until I find where we have a Common Ancestor(s). Once found I sync the Tree to a new project in Roots Magic and after error checking as prior, I drag the home person into my whole tree and merge the Common Ancestor(s). The DNA match and their tree is now part of my whole tree.
I then sync my Roots Magic whole tree back to my whole Ancestry tree.
If you build a DNA match in your Ancestry tree but fail to find a Common Ancestor(s) you end up with what could be a large floating branch, do this with a few DNA match’s and you have a whole mass of unlinked branches.