Xero is a full fledged accounting system where as freshbook is more like a billing system with few accounting things mixed in.
I personally use xero for my small business. It allows me to see a complete picture of my financials for my business. my bills that I have to pay, invoices that are coming in. expenses etc and at the end of the year I generate reports that my accountant uses to do his business.
Xero also links to lot of online systems, I have it linked to insightly for CRM.
As for the bank accounts I am personally in favour of having separate accounts. My company has its own bank account that is used for all business stuff and I draw a monthly salary which I deposit in my personal account. Where I am from we have no taxes etc. So it might be a bit more complicated than your situation.
Other comparable systems to xero are freeagent, kashoo, quickbooks and less accounting.
Let me know if you have any questions and I will be happy to help.