It's mostly luck of the draw whether the heroes decide to use their skills or not. When they use their skills/die, you'll wanna make sure it's in an enclosed space: the more blocks of dirt, the better. Now, when the Mana's abundant in an area, break the blocks in a pattern similar to the way you would spread Nutrients with a Slimemoss. Now, in my experience, Spirits will only deposit their Mana in blocks that have at least one Mana. If the path you created for the Spirit doesn't include a block with one Mana, cull one spirit to force the Mana deposition.
"Waking" the Skeleman/Rune Monster should prevent it from absorbing the Mana you're trying to gather. Just be aware that the Wookiemon will eat any spirits it can find. Side note about them: when they've eaten enough, they'll fall asleep. The trick is to have a deposit of Mana far from the main "branch" of the dungeon and keep the Wookiemon sated with Spirits. If it falls asleep, it won't venture off further in for your OTHER, more important Spirits, and it'll stay out of harm's (and heroes') way. The DEF bonus it gives to your monsters applies no matter where the Wookiemon is in the dungeon, so it's better if it's in a secluded place.
In summation: narrow spaces allow for more Mana to be deposited from hero skills/deaths. When you've got a sizable amount in a given area, make a pattern similar to how you would for a Slimemoss gathering Nutrients. If you're trying to make a dragon, you'll need a long, horizontal path so it can move and incinerate heroes. Does that help?
Oh, and fun fact: break a block with exactly 11 Nutrients and 11 Mana and...