How exactly to HD work?
1 HD = 5 HP
But sometimes there will be a monster with 2 Hd +1 but the total HP won't be 11.
I feel I've confused myself
It's not you. It's Glaive. I don't randomize monster hp as D&D does - who wants to track variable hp for a dozen orcs? I use that flat 5 (though I buff/nerf hp as I feel appropriate).
I still record those little +1/+2 HD bonuses in Glaive because it affects the monster's attack bonus and the amount of XP it is worth. Using the guidance in Old School Essentials, a monster with 3HD has an attack bonus of +2. A monster with 3HD+1 (or 2 etc.) has a bonus of +3. They are also worth more xp, and if they have special abilities those also add xp - which will be a different value with or without the little HD bonus.
Your confusion is warranted. I've never explained my monster conversions to anyone before LOL