I need advice in regards to my employer paying the taxes on my behalf and just writing out a check to me for my net salary.

No, no, and no.  Your (former) employer can't legally do this.

Any deduction from your earnings has to be stated, with an accurate description and dollar amount, for each pay period.  That's the law.  And if you were on salary, you shouldn't be getting a 1099, you should be getting a W-2:  there's a very big difference, because if it's a 1099, you're being paid as an independent contractor, not as an employee, meaning no unemployment insurance payment, no Social Security or Medicare tax, and you'll have to file a Schedule C with your tax return and pay nearly 15% of your gross earnings in self-employment tax.  Depending on what kind of work you do, it might also be illegal to pay you as an independent contractor if your job duties didn't qualify for that.

You need to talk to a good lawyer about this, as soon as possible, and file the appropriate lawsuit.