Gold is for the body. You earn it by killing enemies and clearing waves. Use Gold to upgrade your units, your castle, and purchase basic cards.
Gems are for the soul. They are the premium currency, but here, you can earn them with skill. Gems are used for 'Empire Income' upgrades and buying legendary chests.
Do not waste Gems on skipping timers. Save every Gem you find to invest in permanent upgrades that boost your economy. That is the smart play.
You earn Gems by capturing colonies on the map and by completing daily missions. A diligent Emperor is a rich Emperor.