Your player level progress increases with every upgrade to your apps, device, and network. You earn the most points towards your level with device upgrades, then network upgrades, then apps.
Your player reputation is determined by completing bypasses, password cracks, downloads, and uploads. Only successful processes will earn you points towards your reputation. You earn the most for cracking passwords, then bypassing firewalls, then uploading apps, and then downloading apps being the least. If another player upgrades their Firewall or Password Encryptor level, re-hacking that new level will also earn points towards your rep. If a Firewall is higher level than your Bypasser you will earn more rep points upon a successful hack. Same goes for a Password Encryptor. You wil still earn points for hacking apps lower than yours, just not as much.
Overall Score is determined by a very simple algorithm:
Score = Level * Reputation
So two players can have overall scores relatively similar...but with two completely different reputations and levels depending on their play-style.