If cost of maintenance is an issue, buy something else, preferably oriental. The Ducatisti on this board tend to be gear heads, talented individuals that can do their own stuff and appreciate technical design. They will steer you towards a Ducati because they love the bike, although a less monetarily/mechanically demanding ride might be more appropriate.
If you have money issues and have a shop do all of your work, you will not be a happy camper.
The same thing happens in the automotive world with Ferrari's, Porsche's and older Jags.
Maintenance, even if you have a shop do it, isn't too bad. No matter what bike you have you'll have to do normal 3k oil changes, new tires periodically, brakes, etc. Those costs won't change from bike to bike much. The Ducati's however do seem to need tweaking at the 6k and 12k services that are a little more pricey than Japanese bikes. Other than that I would say your service costs overall are in the normal range of any bike. However, that is going to at least twice what you pay per mile on a car...
An FZ 6 has valve adjustments every 24-26k miles. That means that a ducati will cost you at least $600 more (we are talking 2 valve, not four valve) for the valve adjustments ALONE over the same period. (24k)
You will need to replace sparkplugs on an FZ6 every 8k. Other than various checks, that's about it! Tires, chains, etc. will be the same for both bikes, I think.
On your FZ1 you will spank riders like me with their S4's that cost 11k+4k in mods on the straight but in the corners, it really is the rider that counts. Spend you extra cash on track days and lessons, and you are unbeatable on a budget!
Just a thought. If you are hooked on the L twin and the Ducati cache', then spend away!
I have a 94 M900 and do all my own work on it. If you have the desire to do your valve adjustment on your monster, you can. It is not that difficult. I bought a video from Pro Italia in the LA area that goes through the process. There is also information on the procedure at The Ducatisuite. I think that many people are intimidated by the "desmo" valve actuation. I am trying to dispell that myth and get people that have the desire, to do their own work. I am personally working toward developing the tools to make the process as simple as possible. I have started by designing shim kits which are now available. I also have some other products coming in a few months. My suggestion is to learn as much as you can before you get into it, and then if you feel comfortable, to dive in and do it yourself.