The DI Scoring Program can be configured to support running multiple sites or rooms for teams in one Challenge and Level. The Tournament Wizard includes the Identify the Competition Levels page, where you may define any additional levels you might need.
You might consider some "neutral" names for these additional levels - Elementary for a single-site challenge might suggest Elementary-A and Elementary-B for two sites for another challenge - or Middle might suggest Middle-Red and Middle-Blue.
Some folks believe it feels more "equal" if both separate level rooms have a unique designator (EL-A and EL-B) rather than having one be EL and the other EL-A. And it feels odd to have a designator at all on a challenge level with only one room (e.g., Challenge C, Level EL-A). So this way you might choose to have a level with the undesignated name and as many as you need with designators.
If you have two separate "Tournaments" occurring at the same time, your "customized" Level names might be Elementary North and Elementary South with abbreviations EL-S and EL-N. Remember you'll also need to define these same additions for your Middle Level and Secondary Level teams.
You'll also need to define Advancement Rules (also through the Tournament Wizard) for these new Levels. Once you define a new level, the Scoring Program's Set Advancement Rules tool will automatically include each new Level to remind you to do that, but only the "advance 1 team" default will be set! You must add whatever additional Rules are appropriate for your Tournament!
There is nothing magic about any particular Level designator, but you might be thinking that the capital letters A through E often refer to Team Challenges and therefore select other names for your Levels. Try to keep the abbreviated names short, due to some of the places they're used in the program windows and reports, where there's not always a lot of "real estate" available.
If you employ a spreadsheet to import the teams into your tournament in the DI Scoring Program, use the abbreviated level name text in the "Level" column of your spreadsheet. Your might think of your spreadsheet's Level column as actually being a Room column.