I use the Pro Series Professional, but assume the programs are similar.  If you have filled out the SEP 4.a. box with the amount from one LLC, but it still comes up with the two added together, you can go on down to the Adjustment part and fix it there.  If you need more help, use the HELP at the top of the page and get the Instructions for this Worksheet.  It states that it only does one business at a time so can't understand why they are adding together.  Override or Adjust.  Use the HELP.