Hi. I also have a WarpEngine on my A4000D. Only usefull thing I can share is that I had a bad time trying to get the termination working and ended up finding that some LVD acard adapters don't actually seem to provide termination. Also don't forget that the WarpEngine's termination is passive, but can be disabled by taking off the red resistors on the card (they're detachable). You'll have to provide your own termination in that case. So a thing to try would be to take off the resistors and try active termination, but it should work with passive, just make sure the hd you're using is also set to passive (?).
Can't remember of anything else.. oh wait. I just used the default AmigaOS tools, didn't need anything specific. Maybe the WarpEngine tools don't got too well with later versions of the OS (haven't tried it ) ?