What is the best way to spend your marks of glory on your Building in puzzles and survival?

If you are focusing on one troop type then put your glory into the 3 buildings that buff that troop type and also Buildings that give general troop buffs.

If you focus on one troop type, you'll get a moderate stat boost for that troop. If however you level up all the buildings, you'll be able to use gear refiners to unlock glory refinement which will increase your damage done/decrease damage taken. It will also get you to a higher floor on tuesdays ruins challenge which will earn you more ruins coins every week which can be used for chip promoters or speedups.

Take note that you cannot reassign marks of glory, so whatever you upgrade will stay that way. I'd recommend upgrading everything to at least 20 and then if you want to focus on one troop after that, you can. At level 30 the building related to your chosen troop gives a 60% attack bonus which is not really that good considering the amount of marks of glory it takes to get there