It's all The Plan by Edward.We know that he's been keeping secrets from the agency ("We only found out about this place last year") and we know he's good at being sneaky (how he disposed of the baddie in the pilot), what else is he hiding/planning?
It's all The Plan by Henry.He's the one manipulating events, while appearing to be a confused bystander.
The glitch in the Edward/Henry switch was caused by the computer tech's misuse of the mainframe.First of all, you don't hook up your secret supercomputer to the internet. Second of all, you don't install or play World of Warcraft on it.
Henry is the real personality.If you employ a brilliant super-spy, it's hard to understand how transforming him into an average suburban businessman helps you. But brilliant super-spies can't be that common. So if you could transform someone into a brilliant super-spy, it would be worth it. Even if the technique works on so few people that you have to use an average suburban businessman as your subject.
Neither is the real personalityThere is a third, as of yet unrevealed personality, who is the original. The other two are artifical and dominant.
Tom/Raymond is not being switchedTom is simply a regular agent with a regular cover identity.
Raymond has a rivalry/dislike of EdwardHence Raymond's amusment with making casual threats to Henry.
We haven't seen the last of that Russian guy'Dying' would take him off the radar.
Henry is the real evil side.He's a lot better at acting normal than Edward, and is waiting for the day Edward loses his usefulness so that they can permanently suppress Edward and completely forget about them. Then his day will come. His day... to rule.