Fishbowl Inventory: Online vs. Server application

The small business I work for uses both the desktop version of QuickBooks and Fishbowl.
We have had a rocky start because our initial team member, who was in charge of implementation, had no idea what he was doing and refused to involve any other team members in the implementation. He had used all of our implementation/training hours and was shortly fired after the initial launch. We have spent the past year fixing all the problems the team member created, and I like to think we have a solid grasp of the software now.

The only issue our team consistently has is that the connection between Fishbowl and QuickBooks constantly breaks, and our IT team does a very poor job of monitoring and quickly re-establishing it.

We have been looking into transitioning to QuickBooks Online to help solve this problem, but I am wondering if anyone else out there uses QuickBooks Online and has any integration or connection issues?

We also use SPS Commerce for EDI invoicing, and have been told that if we were to switch to online applications, it would completely change the integration, but would be a much more user-friendly and faster interface.