I like to place the liner so that the thread diameter just misses the face of the plug. This means I can unscrew the plug without having to remove/drill out the liner first.
I try to center the liner in the side flat, top to bottom.
I have lately started to use Tom Snyder's inside coning tools, which have been very satisfactory, especially in getting the touchhole a little closer to the plug. Properly done, the gun performs much as if it had a touchhole liner installed. Eventually the hole will erode, so at that time it can be lined, eh.
Tom