I am a CPA, but not specialize in tax. Here is some information from my previous experience. This is just FYI only.
If you are holding F1 visa, then you are non-resident alien, you need to file 1040NR by filing joint return. You can claim tax treaty, normally $5000 dollar allowance per year.
If you are holding H1B for more than 183 days in 2003, you are treated as resident alien from tax perspective. You can file joint return, as long as your spouse has tax ID or social security number. You need to file 1040 tax return, but cannot claim tax treaty.
You can claim head of household if you meet certain criteria; you can check the test on 1040 instruction to see if you qualify. Normally head of household can get the maximum tax benefit. But you need to be the main person who supports the family; you did not live with your spouse for the past years (similar to this) and your kid lives with you for more than 6 months, etc.
In summary, you should be able to file married jointly regardless, but due to the marriage penalty from tax perspective, you may not absolute benefit by filing jointly. Try different filing status to see if you can get the most tax return before you submit it.
If you are holding H1-B, in order to pay less tax, you should leverage the flexible spending account, 401k, etc. In terms of auditing, there is computer scanning; all tax returns will be scanned to see if there are obvious errors, any policy violations. So you’d better use tax return software, such as Turbo Tax cause the software will perform the same scanning for you. At the mean time, IRS is doing random manual audit as well, but they are so behind the schedule.
The above information is just what I know. It may not apply to you, but hopefully it’s useful somehow. You can also call 1-800-829-1040 and talk to the tax specialist live if you have more concerns. But most of them are not very good at 1040NR and international tax treaty; you need to talk to local tax agent for more detailed information. Ask the main line for the phone number in your area. Good luck.