Customers are regularly checking out as guests then come back in a day or two and creating an account. Is there a way to add their guest orders to their newly created account?

There is no way for Coreware to automatically merge contacts, for security reasons. However, the duplicate merge function within Coreware is extremely powerful and very easy to use. The best way for you to use it is go to:

 Contacts->Contacts, make sure no contacts are selected. Count display should say 0 Selected. If not, go to Actions->Unselect All. 

Then, select, by clicking the checkbox on the left side of the list, the two contacts you want to merge.

Go to Actions->Merge Selected Contacts. That will take you to a page where you can visually check to make sure everything looks right and merge them.

This functions works well and gets used many times every day.