You'll be filing taxes, signing agreements, etc. all as the ACTUAL company name. Typically, you only use a DBA when you expect to have different lines of business, but want them all operating under a single legal entity. Rules for DBA vary by state (and actually will not always be called a DBA in each state, see: Washington), but don't have a federal impact.
One note, if this is really about name changing only, then you might just consider changing the company name and be done with it.
As for Trademarks, that is also a completely separate matter, really. If you have a Registered TM, then you are covered for the industries/purposes of that TM in all states. Your DBA doesn't really matter here, as trademarks are about usage in commerce - not what you named your company.
If it sounds confusing... that's because it definitely can be! To that regard, I would go back to the earlier piece - if you are not using the DBA because you want to have different lines of business, I would consider just doing a company renaming now. It's actually easier the earlier you do that anyhow if you see it happening down the road at some point.