Should I be concerned that my new employer has a pay structure that uses both biweekly wage checks and weekly reimbursement checks to equal my $20/hr?

[nikkijosh06]

The biweekly paychecks will be for a base salary of $11 per hour. Then, the weekly reimbursement stipends in the set amount of $360. Which equals out to the $20 an hour. They call the reimbursement a weekly housing and travel allowance. I just want to make sure that this is an okay practice before I get in too deep with this job. Its a great opportunity and will look great on a future resume, so I would like it to work out. At the same time, I am worried about the legality as I have never heard of this before.

[xmasbaby0]

You need to find out how the employer intends to report that "stipend" income.  Are they including it on the same W-2 along with your other hourly wage income or are they going to put that on a 1099NEC and report it to the IRS as "self-employment" income.  If they are doing that (which is sketchy) that means no tax would be withheld from that "extra" stipend amount and you will end up owing and paying tax on all of that---when you have "self-employment" income you pay all of the Social Security and Medicare amount yourself--15.3% of it will be owed as self-employment tax.   And you would also be subject to the ordinary  federal and state tax.   

In other words---if they pay you that "additional" $9/hour and treat it like self-employment income on a 1099NEC, you will pay all of the tax on that with nothing withheld for tax and no part of it paid by the employer.  Find out now how the employer plans to put  that income on tax documents.   If they are putting all the $20/hour income on a W-2 and withholding Social Security and Medicare and ordinary federal and state tax, that is different.  But you do not want a nasty surprise at tax time.