I would also look at
www.xero.com - totally web based, NZ company now in Australia, handles multi-currency and has direct daily downloads from your bank.
Designed for non-accountants. Free trial then $49/month or $499 a year.
Not sure re the paypal integration but I am sure something could be worked out.
There is also tool to allow Paypal imports directly into Quickbooks that seems to work quite well -
www.bigredconsulting.com
If you want free - use excel to track all expenses, plus the merchant reports from Paypal should be sufficient to show your income.
If you want low cost....ummm, well - you get what you pay for!
Have you actually had written advice regarding your tax residency? It is actually very rare to have residency in both countries - I deal with a lot of Australia / NZ clients and have never seen it before. Do you mean you are simply required to lodge a return in both countries?
Hope my information was helpful.