There are a couple of ways to do this, but what I do for development purposes is to modify my gameinfo.txt.
Under the SearchPaths section, just add a new line defining your mod folder. So if you had a folder in Steamapps/Black Mesa where you wanted your mod to be and it was called “MyMod”, your gameinfo.txt would contain:
game+mod MyMod/
That’s really all you need to keep you mod content seperate from the game files for easy development and packaging, though be warned that full mod support isn’t in yet on account of the BM branch of the engine being based of a post-Steampipe update version of Source. As a result, some existing files really dislike being overwritten and may or may not load ingame. If you find something that won’t load and figure out a way to make it do so, please let the rest of the community know!
As for distribution, I have yet to get that far in my BM maps, but it should be as simple as converting it to a VPK and using the workshop publish .exe.