First, I'm not sure I would take a newly certified diver to Dolphins Den (aka Dolphins Graveyard).
But you are correct. West End Dive Resort is affiliated with Splash Inn, not West End Divers.
West End Divers does have some recommended (but not affiliated) places to stay.
Dive & Stay
The reality is you can stay anywhere and dive anywhere in West End. There are places for every budget and preference. If you want to dive with Splash, they have an economical stay and dive package. If you want to dive with West End, it's more of an a la carte experience but they are excellent.
If you want more information about West End Divers and what's around, send the an email. Courtney Blankenship, the shop manager, is awesome and can answer all your questions.
Personally, I've stayed at Lost Paradise multiple times. It's rustic but clean and charming. And they treat guests like family. Next door is Brisas del Mar - also stayed there. More upscale and renovated rooms. But also more than double the price. Both are easy walking distance to West End Divers. But there are many many other places to stay as well.