I worked almost exclusively on internal inventory systems for the first five years after I graduated from college. These systems were custom built for commercial printers who ranged in size from small specialty shops (think promotional items like pens and golf balls) to large factories with 8,000 SKUs and 12 million pieces of printed material stored in a three-floor building with dozens of rooms. So I speak with a least some authority on this matter I guess.
Once you get the bugs worked out of your program (or you integrate an off the shelf product) the nightmare really begins. The big problem with inventory tracking isn't the software or the system but the people who use it. If your people are accustomed to their method of pen and paper to an Excel doc they will resist a new system initially and maybe forever. If there's ever an error, and there will be, they will blame the software and not a co-worker or themselves. The factory with 8,000 active SKUs has had a bug free system for years now and still, even when a mistake can be tracked right down to the individual who made it, they blame their computers. It's just human nature.
And if your software has bugs then you can pretty much kiss the whole thing goodbye right from the start. One of the projects I worked on was plagued by errors that a no-longer-employeed junior programmer couldn't fix. By the time the cavalry was called in to correct things all faith was lost and never really recovered. Unbeknowst to us, the workers in charge of the inventory started running their own parallel system with pen and paper.
Your problem is compounded by needing to track items across multiple locations but saved by the low amount of items. Yobiz looks pretty interesting. I would strongly suggest going in the web/intranet app direction.
I've gone on a bit long but I just wanted to wish you the best of luck.