If you want to be able 1099-r and 1099-m as separate runs you will need to set up a user defined profile code to track 1099 Type. 

You can add new User-Defined Codes by following these steps:
  1. Go to Tools > System Utilities > System Initial Set-Up.
  2. Select the Mailing Setup Tab.
  3. In the Profile User Defined Codes section you can enter in up to four different labels.  If a box is left blank, the field will not show up on the Profile 2 tab. 
  4. Click OK.
  5. Exit the Profiles module and re-open. You should see the changes take effect on the Profile 2 tab.
Once you have added the Code and made the selections for your vendor profiles you can select based on this field when running 1099's.