Yeah, as Charlie Horse said, don't go hopping about willy nilly. Basically, there are several ways you can do this.
As you've said, you switch to another PoV when your main PoV leaves the room. I wouldn't consider that omniscient, if it is divided by breaks. I don't think it's omniscient even if it isn't divided by breaks, though I may be wrong. Omniscient, as I've always seen it, requires the previous PoV (in this case the one who left) to be in the room and for thoughts to switch back and forth throughout the dialogue and narrative. You can't dip into both character's thoughts if one of the characters is missing from the action. Is this how you are writing it?
Omniscent can get annoying quite quickly. Imagine this: You have an intelligent omniscient narrative, yet the narrative also changes to two separate PoVs with limited intelligence and different speech, and you keep switching back and forth between all three within paragraphs... Yeah, annoying.
So basically a few things:
1. Who is your narrative? If it's in third person, then it's either the PoV or a 'bystander' simply watching. Omniscient works better if the narrator is a bystander and the voice is separate from the thoughts imo.
2. Section breaks are good, if I am correct about the way you are writing (character is MIA).
3. Third person limited (or 'close') colors the narrative in the PoV's voice, his language, his thoughts. It can be hard to experience the thoughts of another by adding omniscient. Uncomfortable to switch from one voice to another voice, then back again. It can be done! I am reading The Wreck of the River of Stars (sci-fi) right now, and it does it quite gracefully. It seems quite hard though and you have to be very careful.