Permanent upgrades are passive. There are actually three I have on my jet:
Permanent Upgrade: Maintenance - what this does is passively increase the rate at which your jet fixes itself. If you equip Maintenance as a perk, the speed of fixing itself is increased further. Note that after being damaged, there is around 5 second delay before your jet will fix itself, this is not affected by either upgrade.
Permanent Upgrade: Air Radar - this one scans the area IMMEDIATE TO YOUR JET and automatically spots passing air helicopters and jets. It works properly on my XBOX 360, with the latest patch and B2K. The Air Radar perk scans the entire battlefield for flying jets/helis.
Permanent Upgrade: Below Radar - this is absolutely useless on a jet, but it works regardless. When flying below radar altitude (which i believe starts when your altimeter flashes red, so at around 50m) you cannot be locked on with AIR to AIR missiles (so, heatseekers and SOFLAM + Javelin). Note that if you're locked on before entering "below radar" it won't loose your lock on, you'll still need to pop your flares.
As for the helicopters all of these do the exact same things with the only difference being "below radar" is incredibly useful for the ZW-11 and the AH "Little Bird". When flying low and mowing down infantry, they won't be able to lock on to you with the Igla or Stingers. Bear in mind, the Little Bird is extremely easy to shoot down when flying low, all it needs is a single M320 to the side to go down to 20% health.
These are all my observations, I might be wrong, I am yet to confirm everything in real terms. Hope it helped!