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I was so glad to see this question, because I wonder the same and it is hard to get good advice.  About 1 out of 3 turbo helpers are helping.  It is crazy that this is not place on the 1065 as a 100% credit.  SO, I have a business TT and a separate personal home tax, and me and my husband are the only 2 ownwers  of our business and we are filing jointly, and I have already done the separate way which is crazy because we are in a community state any way (TX).  So I guess we cant do a standard deduction like I wanted.  There has to be a place for these quarterlys taxes before I transfer all left over funds to our personal income.