I must admit I really have never had an issue trying to come up with different sub settings between music and movies primarily because I think the key is having more than one sub in the mix which contributes to helping smooth out room responses. I generally key off certain music to adjust my bass levels for all, however, there is still the issue of considerable difference in response between Cds, SACD and DVD Audio discs, which I also listen to, so getting it perfect for all formats is pretty difficult just because of the quality of the mix on the disc itself.
The LFE levels you refer to, from my knowledge, only applies to DD and DTS and not the lossless audio formats on Blu-Ray which makes up the bulk of what I watch and listen to anyway.
