I always add a new column, call it "Sorted" and set the sort in that field. If I need a specific filter sort, I will add a new column called "FILTER" field and set it that way. This allows my to better separate and sort my date when merging. I can include or exclude parts as well as sort them. I can even have multiple sort types by including my FILTER fields.
...or...
Filter and sort manually, then save separate XLS files for each sort. Then when merging you don't have to verify the data as anything there is only for that particular sort.