There was definitely some level of cooperation between the two, as the inhabitants of Vault 13 were meant as test subjects for the Enclave.

The Enclave has its fingers in many pies and drew an incredible amount of influence. Is it coincidental that the Enclave’s Whitespring bunker comes as a Vault? Sure, could be. They were the best name in nuclear shelters. Does that perception change at all considering things such as the previously mentioned population set aside specifically for the Enclave? It seems less likely, since it is not a one off deal between the two. So we know the two were in bed together, but it is less clear how close it goes beyond that and how the two saw the relationship. 

For instance, Vault Tec could have been an evil, nefarious company completely independent of Enclave shenanigans, or maybe it is evil as a result of being an Enclave project, even if they do not know it. Currently in canon, there is no indication of what the end goal is for the Vault Tec experiments. Was all that information intended for internal malevolence? Was it meant for the Enclave, just like the test subjects? It is a fair question to ask because I do not believe there is a definitive yes or no answer to the question. 

^This always did bother me. So many entries and details imply so strongly that they were fully prepped to maintain a nationwide presence, actively engaging with some vaults and collecting info from others. And yet… nothing. If I remember right there are even instances where Vault Tec personnel are flat out expecting company personnel to arrive, or keep contact, and it just doesn’t happen. Do they have a secret vault somewhere? Did it all go wrong and kill them off? It’s frustrating that this hasn’t even been partially answered yet.

They do have a secret vault, it's literally called "Secret Vault" but it's from FOBOS so I'd take it with a massive grain of salt.

Ya know, the one Vault we desperately lack in the games, is a Vault-Tec Vault.

Seriously, there's vaults everywhere holding regular people with maybe a few Vault-Tec staff, but an actual Vault-Tec Vault, by the Vault-Tec, for the Vault-Tec as Hancock might put it.... We have none.

Which really makes no sense. Obviously if your one purpose in existence is making and selling bomb shelters, you'd probably make one for yourself.

Unless they have gone to the one place, still untouched by capi- communism!

^^It seems like rank and file employees like the Vault-Tec Rep weren't guaranteed a place in a vault. VT Rep says he was "supposed to win a pack of steak knives" so it seems like the perks of employment at Vault-Tec are dubious at best. Especially when they don't even give you the steak knives anyway, those might have atleast been useful for surviving the post-apocalyptic Wasteland after being locked out of the vault for 200 years.

Still, if he had got into Vault 111, he'd have been turned into a popsicle like everyone else besides the Institute's "backup subject" so maybe he was kind of lucky after all. I'd imagine if Vault Tec did set up a vault for it's employees they'd just end up experimenting on them. It's like the Cerberus Taco Stand except for Vault Tec, if VT opened a Taco Stand they'd put drugs in the tacos and subliminal frequency on the vendor's radio until everyone goes mad and starts brawling in the street. You could pretty much expect the same from anything they do.

Well for the ordinary employee, yeah they obviously probably expected them to pay for it like everyone else.

But what about the big windbags, the rich guys living it up on Vault-Tec's profits, or the scientists that may or may not be collaborating with the Enclave? We know of only one such guy, Braun, who even got into a vault, where he then proceeded to be an online troll for two centuries.

Lol, that's an artful way of describing it. Yeah, it'd be interesting to see what the execs and affiliates had planned. I'd imagine a lot of them would stay away from the Vaults themselves unless they had some particularly sinister plans like Braun did. Those of them that didn't get into life-preservation tech a la House and Bradburton probably lived out the rest of their days in personal shelters for themselves, their family and anyone loyal enough to them personally.

Seeing the myriad of ways those plans could go wrong has a lot of potential.

The secret vault might be the one thing from fallout BOS I’d actually like to see return in some form.