Working from Home

I work from home and make approximately R25000/month. I don't do much traveling and I
manage everything from my desk. I service one company only- I'm basically working for myself. They don't cover any tax etc. and I receive this
payment monthly. What's the best way to deal with the Tax?

Since you aren't a full time employee of the company and you work from home. You would need to register as a Provisional Taxpayer and submit the further two tax returns.