Westbo passes along good advice.
I've used both MYOB and QuickBooks Pro. Of the two I prefer QBP. That may be because my accountant did a better job of teaching me than the person who helped me with MYOB.
It's possible to do everything from estimates to invoices in either application. You can also write and print check directly from both. Not to mention you can balance and track your business income / expenditures / payroll and reconcile with your bank statements via downloads – provided your bank offers that service.
If you go with either of these apps I urge you to pay an accountant to train you and set it up specifically for your needs. Getting the foundation right will make life much easier. It will also make for a faster, cleaner interface with your accountant come tax time.
I know MYOB comes with a book that lists accountants nationwide that are certified to train businesses on the application. Consider finding an accontant who specializes in filing returns for our business. That experience will pay for itself.
If you have questions before buying QBP post them here. I'll do my best to answer. And if I can't answer perhaps another person perusing this thread can help.
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