I use Square AND Quickbooks.
For businesses its all done in Quickbooks as 99% are set on a NET 10 payment. I simply do the work, head to the office and send out an invoice through QB or can choose to do it all before leaving the location on my iPad. As for Square, there are many options. Currently I use it for all residential (rare) and those businesses whom wish to pay on the spot.
I also have links on my website for clients to book online and even for visitors to purchase digital gift cards, all done through Square. You even can have/create a complete Square store.
I personally cannot stand PayPal. They are too buyer sided. That buyer protection is ridiculous.
EDIT: To add. When I first started I did use PayPal. But more than once I got burned because a client would pay for a virus removal but then a few days later get another virus and blame me for not doing the job correctly then they would hit up PayPal to contest the charge and win - ALWAYS - even when I sent in my statement explaining I cannot be held responsible for the person getting reinfected as I cannot control what they click, etc.
I have had only 2 clients do that with Square, and both times I won. Square actually takes my Terms and Conditions into play whereas PayPal could give 2 shites.