To upgrade your Prison, you need Runic Seals.
With each upgrade, you need more Runic Seals.
Below is a list of possible ways to gain these.
Gems
You can purchase Runic Seals using gems.
1 Runic Seal = 15 Gems
10 Runic Seals = 125 Gems
100 Runic Seals = 1,154 Gems
1000 Runic Seals = 10,000 Gems
Campaign Elite Sweeps
You can sweet elite campaigns to pick up extra Runic Seals.
Elite 7-1
Elite 7-2
Elite 7-3
Elite 7-4
Elite 7-5
Elite 7-6
Chests
Chest from the VIP daily clan gifts (Bloodbite city) gives Runic Seals too.
VIP Daily Clan Gifts
You can collect 5 Runic Seals per gift from daily VIP Clan gifts (Once you have level 25 diplomacy for this city).