Good on you. From my own experience and what I've read, you can
drastically reduce the likelihood of knee problems if you:

(1) set your saddle at the right height (a good rule of thumb is that
with the pedal at the bottom of the stroke and your heel on the pedal
[i.e. not the normal riding position], your leg should just be fully
extended), unlike the "BMX bandits" you see with their knees around
their ears. Most riders in the general public (RITGP) have their saddles
too low; only a few have them too high (you can tell because when viewed
from behind, their pelvises rock from side to side - get a friend to
check you out).

(2) use a low gear and pedal faster, rather than pedalling slowly in a
higher gear as many RITGP do. It results in the same bike speed and
therefore the same amount of energy expended, the difference is that
there's less load on your joints (esp. knees), which is better for them
even though they are bending and straightening more often. Racers
typically pedal at 90rpm upwards, but anything from 70rpm upwards is a
good start (you don't need a special speedo with the cadence feature,
just count the rotations of one leg for a minute). The other benefit is
that the faster you train your legs to spin, the more endurance you will
develop and you will soon find yourself able to go faster (i.e. same leg
speed but in the next gear up) for the same perceived level of effort.
In other words, you get fitter faster.

HTH,
One more option that woeked well for a woman that had knee trouble and
writes cycling touring books for Lonely Planet was clip in pedals and shoes,
not cheap but if the above still doesn't cut it it might be worth looking
into. Yet to go there myself but from all accounts are very good.