I'm not sure if a Civic has a stainless steel exhaust system, but if it does, that makes the welding process a little touchy.
It's been a while since I've replaced an exhaust system, but if it's rotted out at all, I've usually gone ahead and replaced the whole damn thing (from the CC on back). Otherwise, it just becomes a patchwork thing that just buys some time, and not much else.