They need to be properly screened and supported by minions. Lots of pillars, mirrors, portals or other terrain to make line-of-sight interesting are also a must. I had great success with a Death Tyrant, but it was supported by a death kiss, a pair of Flameskulls and over 400 hp of zombie giants the PCs had to chop through.

I will agree that for regular beholders tracking what magical effects are suppressed is a real pain. You need to decide ahead of time whether a concentration spell is suppressed when the beholder is looking at the caster, or just the area of effect, as well as whether mobile spells (like moonbeam) can be moved while they are suppressed. Also whether monk ki and Paladin smites are magic, and basically every other anti-magic field interpretation question.