Any thrust large enough to propel a generation ship at a decent speed is going to be easily visible (you can read about Torch Ships to get an idea of the problems of doing this stealthily. They could burn while their ships where behind Jupiter, but wouldn't get up to much in the way of speed.
Solar sails will be reflective and noticeable as well.
Four ways that I can think this might work. Only the first and fourth ones really strike me as super practical.
For some reason the aliens know the humans are leaving, but can't pursue in a timely fashion. Perhaps their ships arrived to Earth after a long journey in a condition no longer fit to fly. Their weapons still work, but their ships are no longer fully "space worthy," or they need to refuel, or anything else that keeps them from immediately pursuing. Any pursuit would take at least a generation to prepare, and by then the humans have a large Delta V lead.
** Method Two **
Rail guns on Ceres originally used to launch asteroids towards Earth for mining instead launch asteroids out of the solar system. These asteroids have humans living inside, but are not generation ships. Once out of the solar systems they use small thrust to maneuver closer and link up.
Smaller asteroids near the edge of the solar system are simply hard to detect. There is a decent chance they don't reflect much in the way of light, and if the humans are careful won't emit much in the way of heat. So if the aliens are preoccupied with fighting humans on Earth, they may not be focusing too much observational time to look for unpowered objects moving away from the solar system.
They can afford to go slow at first because they are already planning on effectively spending forever to get anywhere. However, a full generation could pass before they were at a safe range to link up and begin thrusting for real.
Actual numbers are impossible without having more details about the aliens and just how technologically superior they are to humans.
Deception. They burn hard, but do so to intercept comets, asteroids and other objects already leaving the solar system. Land people on them, burrow in, and then hope for the best. At some future time build and activate thrusters on your new home.
Now, the problem here comes in not being super obvious. If your people are clever they might be able to burn to match velocities with these objects while sight lines to Earth are blocked.
While I see this method being interesting
Over whelming numbers. You scatter in every direction. Space is big, and Newton is their friend. An alien ship might hunt down and kill a human ship, but for it to then reach the next nearest human ship might require massive amounts of fuel. Launching from the asteroid belt already gives the humans a huge delta V advantage over the Earth's gravity well. Maybe the majority of the ships get hunted down and destroyed. If even 10% survive, that could still be many humans.
I lied, here is another method that would work. Just run. The aliens might notice them, but it doesn't matter if they can't catch them.
One thing to note about relativistic projectiles. It takes light about 8 minutes to travel an AU. If the humans did a synchronized launch from Jupiter, the aliens would not even know for between 52 and 36 minutes depending on where Jupiter and Earth are because of the light delay. At that point they could launch projectiles at near light speed
If the humans are pulling an uncomfortable 3 gees during an initial "Holy cow, lets get out of here" speed burst, they will be going at 93km/s faster (3% speed of light) than they had been going by the time the aliens know they have started accelerating (During which time they can have changed their direction). During that time they will have been able to travel about a tenth of an AU!
How are they achieving such awesome accelerations? Fusion power perhaps. Or maybe they are harvesting naturally occurring anti-matter from Jupiter's magnetic field. Of course they will run out of this quickly, and then away from Jupiter can no longer get more and become stuck on the slow path. But by then they already have a decent lead and can just "random walk" their ships to avoid non-guided ordinance.