The wires which you mustn't mess with are the incoming wires from the exchange, which should connect into the back of the NTE5 base. The wires connected to the faceplate are yours to do what you want with.
A filtered faceplate has two sockets on the front - a normal telephone socket (for a telephone) and an RJ11 socket for the cable which connects to the router. You don't need ADSL filters on the extension sockets, because they are already filtered in the new faceplate. But if you have a Sky box connected to an extension socket you might benefit from using an extra filter on that socket to improve the filtering of the Sky box.
If you have crackling on the line, a filtered faceplate won't stop it crackling. It's probably a line fault (intermittent, perhaps) and you should try to get that fixed first.
There are several different makes of filtered faceplate, but the ones generally considered to be best are from
ADSLNation and
Clarity.For a one-off job like this you might as well use one of the 50p cheapie tools, unless you really want to invest in a professional one.