They don't pay. It's supposed to be some combo of favors owed to the party that get you upgrades. The GM can explicitly plot some of this, just let it happen in the background, or introduce a background patron (salvage company you report dead ships and big items you can't drag off?) who pays for ship upgrades without asking much of you in campaign.
My players get their Tier 1 ship as they escpaed from an exploding station (it was a half build transporter in a dry dock).
They then managed to fight of some pirates and salvaged their ships.
So the first upgrades (T1 > T2) were not really upgrades, but more repairs and installing the salvaged items. This was done and payed by the Absalom Station as an reward, because they managed to rescue many people from the exploding station.
They also got a small update (better computer & shields) as a bonus because they joined the Stewards afterwards.
Their next upgrade (T2 > T3) will be a refit done by the Stewards for their next assignment.
I want to try not to make "hard jumps" from one tier to the next, but give them a new systems as a reward during the game (most times they can choose it). When they hit the next level, their ship have ~ half the next tiers BP spent already and they can then spent the rest as they like.
For me this feels better, then a simple: *Ding* you can assign X BP now!
What if they are in the deep, dark depths of space, exploring the unknown, nowhere near any known civilization? Are they still inexplicably able to upgrade their ship somehow? Do you simply retcon that they happened to have the parts and expertise on board from some previously unmentioned background scene?
