I have a regular job, but I also earn 20-30k on the side through side projects(1099 work). Given that I am running a business is there any difference in how I can deduct charitable donations versus regular salary workers?
If your business is not an LLC or a corporation, you cannot take charitable contributions as a business expense. (And as you don't give 1099's to corporations, I'm guessing you're not one.) Pay yourself from the business funds, then use this income to make charitable contributions. You then claim the deduction for charitable contributions normally.
Note this means that unless your deductions, including the charitable donations, are more than the standard deduction, you don't get any tax benefit. I don't know how rich you are or how much you give to charity. With the recent increase in the standard deduction, you may not be able to claim anything.