Self employed courier - best arrangement?

Shade-

Hi all,

please bare with me as I'm not that good at understanding tax arrangements. 

I'm starting a new job as a self employed courier next week for an Amazon Delivery Partner and they offer 2 methods for payment. The first is a simple invoice system, the second a tie up with an "accountancy firm" called Securitax. Looking up their track record online it's poor at best. Seems they have some very dodgy VAT records in particular. The company insist that using their deal with Securitax will actually leave me with more money in my hand but I'm not convinced. 

The question is, if I choose their simple invoicing system how do I go about filing tax returns and making sure I pay the right amount? I obviously want to get as much deducted from my tax bill as possible too so how do I go about putting expenses such as my phone bill, home office (I do have one), uniform washing etc?

I know this is a bit of a rabbit hole but I'm completely new to being self-employed and want to hang on to as much of my cash as I possibly can. Thanks for any help.