Hi,
It's not clear why you need to do anything with the Linux driver. If you want to have multiple endpoints with the same configuration, udev rules can be used to prevent the device files' name collisions. If you want to do periodic access -- that can be done from the user space as well. If you're unhappy with the device files a single core supplies -- make a custom one in the IP Core factory.
So why do you feel a need to play with the driver?
And by the way -- you didn't mention if you're working with PCIe or a Xillinux-based platform.
As for latency -- there have a few teams of Physics professors researching plasma reactions using Xillybus, working with latencies as low as 30-50
microseconds with userspace programs, so your 20 ms intervals should be more than possible. Odds are you'll have no problems at all with that.
For some guidelines for proper low-latency programming, see
http://xillybus.com/doc/xillybus-latencyRegards,
Eli