I have a small set up at home with a Fluval 2 Plus canister filter.
The instructions with regards to filter maintenance are unclear (or
I'm stupid) so I'm seeking advice here.

I did a 25% water change today and tried to clean the filter. I did
this by removing the sponge filters and rinsing them in the water I
had removed. My question is how hard should this rinsing be? My method
of rinsing basically removed just large debris such as plant leaves.
The filter medium was still brown in colour and has a fine brown
sludge in it. I am nervous about cleaning more vigarously as I do not
want to remove the bacteria which I believe live in the filter (or
have I grabbed totally the wrong end of the stcik here?).

The instructions also say that the filter medium will last 4 months
before needing replacement...I am assuming I do not change both pads
at once as this will certainly cause the tank to go into cycle again,
won't it?

Any advice is always appreciated as I know you guys really know your
stuff!

Dunno about "really knowing my stuff" but here's my two cents! I've been
using canister filtration (among others) for about 7 years and have been
fairly successful. Water parameters are stable and the fish often breed.

I don't clean the filter every water change - more like every three months
unless the flow seems to be restricted. I have used Fluval filters in the
past but now use Eheim, and I believe that this is the schedule Eheim
recommends.

Like you, I also rinse the media in water I've just removed from the tank.
Some folks don't feel that this is necessary, but I figure what the heck - a
little chlorinated tap water can set your biological filter back a few
steps.

I tend to rinse the sponges fairly vigorously - squeezing them out a few
times to get most of the "sludge" out. If your media fills up with sludge,
it reduces the total surface area for bacteria to colonize (it may
ultimately "smother" your existing bacteria - not providing adequate
oxygenation) and ultimately reduces the flow of your filter. As for
rock-style media, I will generally swish them around in a pail of water
quite vigorously to remove what I can.

I generally use sponge media for quite a long time - I've used sponges for a
couple of years without any apparent adverse effects. Obviously, if it's
visibly deteriorating and can let water flow by without being forced through
the sponge, you should replace it.

If some of your media is highly porous rock (intended for biological
filtration), it's generally a good idea to swap out *portions* of it every
once and a while to prevent it from getting clogged and therefore less
effective over time. By only switching say, 1/3 of the media, you don't
lose too much of your filtration capacity and the new media is seeded by the
existing stuff. Personally, I switch out a portion of that media every time
I service the filter (approx. every 3 months).

I often clean the mechanical media under the tap to remove all the "goo"
that I can - the bacterial colonization here is the least dense, so I'm not
as concerned about it.

Overall, this approach has served me well over the years.

Hope this helps.

- Rob