Hi kflynn and welcome to the forum.
Some thoughts and some questions.
First a question. Which version of Monarch are you using? I am hoping you will respond that it is V9 since your requirement for the Excel export would be much better handled by V9 I suspect.
The output you seek looks to me very much like that you would obtain by ignoring the Total Lines presented on the report (which presumably summarise the details above them) and getting Monarch to provide the subtotals by internal calculation using a Summary with sub-totals at value changes in specified key field(s).
One danger is extracting the total lines from the report is that if you subesquently apply filters (for example) you may exclude detail lines resulting in the Totals/Subtotals not adding up to the same value as the retained detail records.
Bear in mind that when you create a footer record and define fields within it the intention of Monarch is to add those fields to the detail record, which is what you are seeing. It would be useful if you wanted to, say, display a value of the detail record as a percentage of the sub-total and/or total of values for all similar records.
Does this help at all? Let us know if you still have no way forward.