I'm going to chime in here, as other have.
I'm an S-Corp as well, vs. a LLC for exactly those reasons. Namely I pay myself a standard rate, and bill out at a higher rate. There are several advantages, and caviets.
Let me jump in a say that MOST contract houses run at the 1.8 to 2.1 factor and for good reasons. For example, say I'm at a 2.0 factor. If I want my hourly rate to myself to be $40 I'll charge 2.0 times that to my customer, or $80.
The best reason to stay in that 1.8 to 2.1 range is that it is easy to account for in case of an audit. Most GSA have base * overhead * profit, where profit is supposed to be only 15%. However the overhead side of the equation is big, because it covers all the indirect employees; secretaries, accountants, IT staff, CEO's, etc. So on any given GSA contract, the billing rates will all end up in the 1.8 to 2.1 range.
1) The key here is the IRS knows GSA, so anything in that range is legit, so long story short stay at or ABOVE the 50% mark for your hourly rate vs billing rate if you want to stay off the IRS radar.
2) As much as you'd like to, don't ever write off part of your house on the S-Corp. Yes its legal, but since it is highly abused your more likely to be flagged for an audit.
3) Expense as much as your toys as you can, computers, routers, printers are all valid deductions of the S-Corp income.
4) Use quickbooks and its payroll add-ons. Yes there are other tools, but quickbooks is easy an worth the $300. Wait for a good sale in Feb of almost every year for $100 off.
5) Set everything up hourly, not salary. Set your billing rates, pay rates, vacation rates, even 401K or 408K per hour. This just is much easier to track and bill your clients, and pay yourself and your future employee's!