If you want to be able to run for a long time it basically comes down to genetics for a lot of things. If you are in great biomechanical shape (very lucky) it won't matter what you do your knees should be fine. However, if you are like most people then you will need to keep your weight down to lessen the pounding on your knees. Honestly though it sounds like you are more interested in overal functional fitness. Running for a long time is a very very small part of that goal. Running a 5 or 10k two or three times a month is really plenty and will have no negative effects to your joints. But again, if you want to run a lot then you either need to be lucky or you will have to lose quite a bit of weight imo.
If your overal goal is Ultimate then I really really encourage you to run very little.
www.crossfit.com is without doubt the best sort of training regime for a sport like Ultimate (high sustained power output, sprinting, explosive functional strength, and flexibility). A typical program of lifting a few times a week and running a few times a week is not going to meet those goals at all.
edit: what does your torso look like? Can you grab a handful of skin/fat around your stomach or can you see the outlines of your ab muscles? AFAIK most men's 6-pack begins to become visible around 12-15%bf so if you can't really see it than you have lots of room to drop weight. A well defined 6-pack on most men usually corresponds to a bf <10%. Getting to that is a pretty managable (and very healthy) goal.