I just ordered a new cooler line assembly (lower) since the current rubber portion was punctured by a piece of metal protruding from the right side of the radiator. Stranded and ATF is all over my engine and driveway. I've never worked on a car before but after some thorough research Ive decided to repair the problem myself. Slightly nervous ... is there anything obvious or not so obvious that i should look for during this process that is particular to the 98 bonneville. Also how important is changing both lines when only one is leaking?

If the other line isn't leaking, it is fine. Just make sure you use 2 wrenches when removing both ends of the cooler line. One wrench to hold the stationary fastener still, and the other wrench to remove the cooler line nut.