Hello, I recently started a side business outside of my regular employment last year and I am confused on how to file. Do I file them separate?

You would fill out your Tslips (regular income)under your Income tab then proceed to Self-Employment and enter in your small business information. You will need an industry code, this will tell the CRA what "type" of side business you have. Here is where you will find the proper code https://bit.ly/2A9dwtd.