I think part of my issue when building is when I think of checks, I think of “can repeatedly come in without losing eventually,” which I suppose is more in line with a counter as opposed to a check.
Yep, something which can come in repeatedly all over again and can beat the opposing Pokemon is deemed as a true counter. There some nuances like softchecks as well, which may be stacked on a team to cover a specific opposing Pokemon your team finds yourself weak to. In a post above Finchinator and I explained a scenario with Assault Vest Melmetal and how it can serve as a (soft)check to cover Tapu Lele, Kyurem, Tapu Koko, and Dragapult as example. This would be the closest I can personally think of at the moment.
I struggle to find the balance between putting stuff in that reliably deals with what it needs to deal with, and not trying to overdo it and becoming super weak elsewhere.
This can be managed after some time when you're more and more experienced with the teambuilding step itself, which can take time, but in overall if you find your way and playstyle / archetype it gets easier and easier after a while and then you can go out of that section to try and build with other Pokemon since you have gained the experience overall.
Spikes (unless it runs boots in which case its longevity isn’t an issue as much) definitely can hurt Tran
Heatran rarely runs Heavy-Duty Boots, its more reliant on the Leftovers recovery it gets to come in and do its job as a stallbreaker or entry hazard setter. Some Heatran run Choice Specs on sun teams as example, as a Specs-boosted Eruption under sun can definitely hurt even resistent Pokemon.
To your question with a valuable Spiker: Mew can threaten Heatran and Corviknight alike with Taunt in its arsenal. Therefore it can secure that the Spikes remain on the field.
Like I said, probably obvious and I sound like a child,
Not at all. It's always good to think about different scenarios and what you can do and how you can react to these, this is what improves yourself in both the building- and playing-part alike :)
Intimidate Qwilfish and maybe like specs Omastar in rain seem interesting
Qwilfish can serve as a Spiker but it is more viable in lower tiers such as PU, a valuable Spiker on Rain could be Ferrothorn, which also gives the rain team some sort of a Grass- and Electric-resist and a valuable switch-in to Pokemon like Tapu Koko and Rillaboom, which otherwise highly threaten rain teams. Omastar can work in rain, but I would more rely on the Shell Smash set, coupled with Spikes and with rain up it can turn into a deadly lategame-sweeper.