(1) 1099 is for contractors that is true but you can do part time contracting on concurrent H1B provided it is approved but in your case it is applied. That complicates the things. A full time H1b should be always on W2.
(2) (a) Taxes on W2
Taxes on W2 = Tax paid by Company(SSN,....) + Tax...
Re Concurrent Work
(1) Your Concurrent H1b Should be approved before you file taxes on 1099. It should not be in applied state. You did right thing to extend your taxes It better to pay with penalty.
(2) Your work hours should not exceed what were stated on concurrent h1b
(3) Since your...
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