Live in California, work remotely for IL non-profit school

I started last August and have had only IL taxes taken out. I'm expecting that CA will get its share from me, too, when I file.

I am going to assume that you didn't live in Illinois before you started working for the company, and that you didn't spend much time in Illinois once you started.

Yes, California a will want their tax money. Depending on how much you owe there could be penalties or interest.

A tax form will also need to be submitted to Illinois to get back the money sent to them. They may ask for proof that you were remote. Your employer may have to supply an official letter.

Going forward if you are to remain an employee:

• You should ask your employer to stop having Illinois income taxes withheld. Otherwise you will have to get a refund from Illinois every year.
• You should ask your employer to withhold California Income taxes. If they aren't able to do that, you should look into quarterly payments to California.

Employee vs Contractor. Have two area that need to be considered. Which one are you and which one do you want to be.

Which one are you depends on the exact job you are doing. One test is who controls your schedule. If you edit their online presence, and you can work anytime you want, then you might be a contractor. If they require you to be online teaching classes for 5 specific periods a day, then you are probably an employee.

I don't receive benefits - no medical, dental, retirement, etc. I do get paid holidays and accrue paid time off. That's it.

Do you work enough hours that Federal or state law (Illinois or California) would require some benefits?

There are also tax issues that need to be considered. Even if holidays and PTO are the only benefits you still need to factor these in when you negotiate your contractor rate.