If you wish to add different markups to subcontractors, you can do this in Comparisons, even if you do not have subcontractor quotes added.
Go into Comparisons and open the required trade. If you want to adjust the rates you have entered in Estimating, rather than received quotes, follow these steps:
Add Own Rate and a manual subcontractor name. What that name is doesn't really matter. Click Close
Use O to plug the subcontractor's rates with those from your own rate
In the Adjustments menu, go to Adjustments
You can now enter % or total adjustments for the subcontractor(s) in the list.
Once you have finished, in the Rates menu, go to Update. If you are amending your own rate, you should chose Append Nothing in the name options.