Off the top of my head, this is the method I have used in the past. There may be some points that others can correct me on.
Fire up Wally and open Half-Life's decals.wad
Open one of the exiting textures and click the 'Colors' tab in the top menu. Click 'Save Palette...' and stick the .pal file somewhere you can find it again later.
Now, make your decal in photoshop or another graphics app of your choosing. Stick to greyscale and remember that the darker the colour, the more opaque it will appear in game.
Copy the image when you're done and paste it into Wally to create your texture.
Then open the texture and go to 'Colors > Load Pallete...', pulling in the .pal texture you saved before.
Then, click 'Colors > Edit Pallette' and you should see that it is a greyscale series of colours, with the bottom right being a certain colour. This is the colour that will appear ingame. For the blood, this should be a dark red, for alien blood, yellowish green, etc.
Hope this is clear enough. Sorry for assuming you were using Wally, but I don't actually know what else there is...
NOTE #1: Ideally, you need to use the filename decals.wad in your custom mod folder in order for the engine to refer to your custom decals rather than the regular ones.
NOTE #2: I would refrain from adding NEW textures to your custom decals.wad as this can cause issues in game. (Blank white squares appearing in some cases) For the best result, I always just replace the existing textures.