if you are using a line output converter then yes you should splice into the wires after the factory amp. and where to splice is really up to you. some people have spliced into the wires just after the amp...like me and some have spliced into the wires further on towards the speakers...i felt it was easiest to just tap into the wires right behind the glovebox where the wires are easy to get it....relatively...i also had thought of a line level converter but since my amp has line level inputs...i would have been adding another $30+ expense onto my system that wouldn't have an effect on sound quality or atleast not a positive one...in fact if your amp supports line level inputs...i've heard some good advice on avoiding a line level converter b/c it could add signal noise and distortion...I've not had any problems with my system and love the bass...and it's free of distortion issues until the factory headunit hits that brick wall at like 20 something clicks of volume where the factory hu begins to distort audio output
but if your amp will not support speaker level inputs...then you will have to convert to rca style low level inputs...