Important is how much an upgrade is worth.
upping a bone dragon gives it only +1|+0, while upping a flesh spider gives it +3|+0.
and don't forget that some upgrades can change the use of a card. (rage pot, nova, accel).
for example, upgrading a lobo would be my 1st pick in this deck.
While it has no direct effect, if you need it more than once you get the biggest quanta advantage.
another point is shields- while having them cost 1 less is nice,
but you can get the same advantage by upgrading a pillar.
However, the quanta boost from towers can also be spend elsewhere.
remember to consider the QI at all times.
If you start upgrading pillars/pends, you may be better of with -1 or -2 pillars at some point.
However, if you then start up dragons/immortals, you may need that quanta again.
Finally, remember to also split-upgrade pillars and pends, as EQ protection.