Note that both games reference the same uimappings.settings file, in your Application Data folder's Settings folder (well, in your Sins Application Data folder). You don't need to mess around with it, but loading up Entrenchment will reset your settings and vice-versa, which is a huge eyesore and very frustrating.
To get around this awful problem, I have a shortcut on my desktop to the Settings folder, where I have four uimappings files, all of which I have set to "read only" (since I have them set up). I have uimappings.setting, which is for what I'm currently playing (Entrenchment), then I have uimappingsREG.setting, uimappingsREGULAR.setting, and uimappingsENTRENCHMENT.setting. The last two are just backups in case I mess up the other two.
When I want to play Regular Sins I just rename uimappings.setting to uimappingsENT.setting and then rename uimappingsREG.setting to uimappings.setting. I do the same in reverse for Entrenchment. It's completely retarded that we should have to do this, but that's the only way to save your keybinds and play both regular Sins and Entrenchment.