if u use pulvy, upgrade it ASAP
if u r planning to use puppy's deck, upgrade the SoGs and permafrost shield first
after that, i would upgrade the pillars, they can make a big difference
then, i will upgrade cards that can cuts 2 quanta cost, like Rain of Fire and Bonewall
lastly, upgrade cards that doesnt help much after upgrading such as Bond, PA, quint and sundials
for myself, i like to upgrade phase shields after oty and hourglass, i think 5 quanta cost is a lot better
I never upgrade boneyard, but thats up to u.