I am on H1b of an employer and I have received income from the same employer on W2 and on 1099-MISC (same employer). He says 1099-MISC income is a per diem.
Same employer has also filed my green, which is in process and I-140 and I-1485 were submitted two months ago.

I have read several forums and it seems like 1099 is for an independent contractors, which I am not, and should not be given to a permanent employee.

I have three questions
1- How do I file this 1099-MISC income for 2008 TAX?
2- Am I allowed to receive per Diem on 1099-MISC.
3- Does the TAX filing of the per diem income reported on 1099-MISC will/may effect my immigration case? And can cause any rejections or RFEs?
4- Is anyone aware of any professional service available out there specialized in H1b taxes?

Form 1099-MISC can be used to pay per diem.

If it is over $400, you should file a Schedule C with Form 1040NR. Your per diem expenses should exactly match the per diem reimbursement, resulting in NO tax liabilities.

It will NOT affect your green card application.

I can prepare your return if you have not already filed. If interested, PM me.