1) If you are working on W-2 with Company- A means,your H1 should be with company-A.
Here your pay will be little high,means less deductions or less commissions.When your company-A getting 50 bucks from client then they keep 10 or 15 bucks their commission and your W-2 will be generated for 35.
2) When come to Corp-to-Corp(C2C) means your vendor company have tie with your employer Company- A.
here your pay will be less.Vendor company keeps soem commission from total rate and again your employer Company-A will also keeps its margin and pay you the remaining rate.
Here out of 50 bucks vendor comepnay keeps 5 or 6 bucks and remaining 44 will get your employer Company-A,then he again keeps his commission 15,then finally it will be 30 or 29 on your W-2.
I hope you got it.
Note : H1 people SHOULD only work on their employers(Company-A) W-2.For few jobs C2C doesnot works.
Most of our Desi employers have tie with American companies or vendors,so in this case you have C2C oprtion.Clients keep their direct contact with American vendors,very few desi's have direct supply with clients.