The term "1099 Employee" is used often, but in reality there's no such thing as a 1099 Employee. You're either an independent contractor or an employee. If he's a bona-fide independent contractor, and they wish to pay him more, he can add it to what he bills them. If he's not a bona-fide contractor, he should be on a W-2 with all of the benefits that employment brings (FICA matching, worker's comp, other statutory benefits, etc).
The FLSA sets forth the criteria to determine worker classification - you can read more here: https://www.dol.gov/whd/regs/compliance/whdfs13.htm
