The math works the way you think.
Regarding paying FWH on the 941 vs 1040-ES, either way works fine.
Sometimes you can't pay enough federal income taxes on a 941 so that means you need to do 1040ES vouchers... and if you're going to do them anyway, maybe you just take care of all your federal income taxes in one place... on 1040ES vouchers. That's one issue.
Sometimes, too, it's nice to keep the tax liability shown on the 941 below the de minimis threshold ($2500) so you can
not fiddle with EFTPS... and so that can impact your thinking on paying federal income taxes.
Example: We have cheap ebook we sell that describes a "quick and dirty" payroll system that works for many small time S corporations with a single employee. The "system" suggests you pay $16K a quarter (max) and then take out only SS and MC which means a $2448 tax deposit. Because the deposit is low, you don't have to do EFTPS... but then you need to deal with the federal income taxes on 1040ES vouchers.
P.S. The math and example forms are shown here:
http://evergreensmallbusiness.com/quick-and-dirty-payroll-for-one-person-s-corps/P.P.S. I've had professional experience with the IRS losing giant EFTPS payments.