I had mareks...2 cases, both started with limping on one foot. They were keeping the toes on one foot curled in like they were holding something...I had to cull them both within a month of the limping because they kept losing mobility. Neither one ever acted sick, or stopped eating or drinking. they just lost their ability to move around.
Once you have marek's all your chickens have mareks...even the ones that don't get sick..they are just carriers and are able to deal with having the disease...It is the same as vaccinating them...
You will probably do better to just keep on going and cull the ones that get sick, and leave the rest alone. Or just keep hatching eggs from your current chickens, since an immunity can possibly be passed to the offspring. Eventually your flock will be immune to the strain of marek's that you have...but there are many strains, and one of those could sweep in and start killing chicks again...
Even vaccinating is hit and miss if you have already had a case. Any adult birds you still have, have the disease and will give it to other chickens they come in contact with. Some chicks will be affected while others won't. Vaccinations give chicks the disease on a small scale, so they are better able to live with it. Whn they get the disease form a vaccine they don't shed it the way that chickens with the actual disease do, but it all ends the same either way. The vaccination can take up to 2 weeks to take effect, so there is still an infection window in there. Marek's is something most people who keep chickens will have to deal with at some point...even if they don't recognize it for what it is. Most adult birds have been exposed to some form of the virus at some point in their lives and are usually safe. It is chicks that are prone to symptoms and dying.
As for the question of how to vaccinate broody raised chicks, there is no reason to really...because the mom already has marek's. The chicks will be more resistant to it...and they have a natural immunity for usually the first 3 weeks after being born, so you could vaccinate them when they first hatch and then carry on as normal...it might keep the number of affected birds low, but really it will be hit or miss. Some chicks will be unaffected but have the disease. Some will have it and die...It sucks, but it is the nature of the disease.