Get full length fenders, not the trendy shortie MTB versions that are a poor excuse for them. On the front the fender should attach at the crown of the fork and have stays going down to eyes at the dropouts(assuming you have a fixed fork and not a suspension one). On the rear, the fender attachs to the the brake bridge, the chainstay bridge and eyelets at the dropout.

Full-length fenders on the front are designed to protect your shoes and chain/chainrings, and reduce the spray thrown *forwards* and then up into your face. On the rear, they reduce the rooster-tail effect that gives you the skunk look, and secondly interferes less with riders coming up behind you or you have just passed. You can fashion addition mudflaps from the plastic of large milk or juice jugs.

Bear in mind that in heavy rain, you and your bike are going to get wet all over and fenders won't help much. However, overall, you will be thankful for the reduced wear and maintenance costs on the drivetrain. Plus full fenders and mudflaps add to the geekiness and lower the risk of theft.

Just another thought on a new bike (whenever that may be). Front suspension forks that actually work and are durable cost a lot. Otherwise, quality and usefulness are dubious. They also reduce the ability to fit full-length fenders, although it is not impossible with a bit of ingenuity. I always recommend fixed forks for their zero maintenance cost and ultimately, comfort when specifying an urban commute bike.

Finally, be careful with your bike shop. The comment about an entire shifter/derailleur/chainring replacement sets off the alarm bells for me. Get a second opinion from another LBS if you can.