When you say "set up" I assume you want to use Spirit as a base for your mod.
Spirit of Half-Life is a mod like any other. The directory should be placed in your steamapps/common/Half-Life directory. If you want to map for it, then point JACK/Hammer to the appropriate mod directory like so. (You will want to rename the directory to your mod's name though, save having to change all of this later.)
When adding the game data files, rather than adding the halflife.fgd from the JACK directory, use the spirit.fgd in the spirit directory. (Ours is renamed thecore.fgd in this case because we've made code changes, the default is spirit.fgd)
After that, assuming you've done the usual setup correctly, you should now be able to start mapping with spirit's entities.