Reconciling Budget catagories (DC orders)

So I had no idea you could put DC orders in MLS with the "not a check" option in expenses. If I go ahead and do that, is it going to mess up my monthly reconciliations from the past?

Short answer - no.

Longer answer - entering these expenses is part of the reconcile process. If I were you, I would at least enter all expenses starting Jan 1 2010. You still reconcile without doing this because they are charged to your budget account. All budget transactions have a net value of $0 - for each expense there is a corresponding transfer that balances it out. However, it is important to enter them because your budget report is inaccurate otherwise. You will think you have more money remaining in your budget than you actually do, meaning it is more likely you will spend more money than you have been budgeted.