Is this a report? If so, a calculated field would be easier.
If not, there are a few ways to deal with this. They all involve the basic premise of:
select (select sum(col) as Total from Query1) - (select sum(col) as OtherTotal from Query2) as NewTotal
This could be done in a collection of subqueries like above or you could do it in a cte. Either way, that is basically what you need to do.
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Understanding and Using APPLY (Part 2) - http://www.sqlservercentral.com/articles/APPLY/69954/