The big difference between online and desktop is that you can have unlimited companies on desktop. There are some other issues, but for me that is the big one. As far as where to get it, just go to Quickbooks website and buy it. I usually upgrade every other year.
Each note is a fixed asset and if I am going to keep it short term, ie 5 years or less, all the expenses go into a holding account, which is another fixed asset. At the end when I sell it, the fixed asset and holding account are zeroed out. This is very important in regards to advances. If I have to pay the property tax in November, is it a deduction? Sure, until the borrower pays it back in April. If I deducted it in the previous year, then the repayment is income and I'll have to pay taxes on it. So do not expense that stuff. Toss it into a holding account. That includes Servicing costs, loss mitigation, insurance, etc..
If a note becomes a REO, I zero out the note accounts and create a REO accounts. If that REO becomes a rental, I zero out the REO accounts and create rental accounts. Why? Different expense rules along the way. And a rental has different asset accounts, ie accumulated depreciation, land, building, improvements, etc..
Each note or rental is a Class. That was I can have one set of books per company with many notes and I can run the report by Class to see how each asset is doing as well as the company as a whole.
If you don't know how to keep books, get a bookkeeper. The biggest thing to know is that all of your expenses have to fall into one of the categories on the Schedule C. I took the Schedule C and built my expense accounts around that. Now when my CPA gets my books, everything is already categorized for him.