I actually use both the desktop version and the online version for 2 of my clients. The one that I use the desktop with gives me access to her computer via GoToMyPC, which can get a little hard at times if the client is trying to use her computer and I am trying to do her books.

My other client started out using the desktop version. We were file sharing back and forth for quite awhile until he decided that wasn't the best way to keep track of his company files. We switched to online about a year ago. I am so used to online now that it doesn't bother me to go back and forth. The online version is a little different and takes some time to get used to. The layout is a little different and the way you access different parts of the program take some getting used to.

If I had my choice, I would chose online for sure. It is secure, there is no need to access another computer and no need to send company files back and forth. The downside is that there is a monthly fee for this version, where the desktop is a one-time fee.

I hope this helps you and if you have specific questions I would love to answer them for you!

Stacy