System Upgrades will require a combination of System Parts, Silver, and [in later levels] Advanced Parts.
System Parts can be claimed from the Flight Pass, can be dropped in crates, and available as shop offers. System Parts are shared for use across all your aircraft as needed.
Advanced Parts can be earned similarly to system parts: Flight Pass and Crate Drops.
Bonus: Make sure you log in to the web shop every day and claim your FREE Advanced Part!