Cityboy,

As mentioned, Amtrak doesn't carry checked baggage on Regional trains. You are allowed 2 carryon's, so if you don't have anything else you could consider just carrying them on with you.

If there is some reason that you must check bags, then Amtrak would put those bags on one of the long distance trains when they come by. If you want them to be waiting for you in DC, then you'll have to look at the schedule and arrive at least 30 minutes before the closest long distance train to your train. The alternative is to wait in DC until the next LD train comes by. But either way you're going to have to wait on one end or the other if you check your bags.

I should also mention that being you're only going Baltimore to DC that you may find the agents in Baltimore reluctant to check your bags for such a short journey.

Are you connecting to another Amtrak train in DC? Because that would change things!