Cash is better than cheque because it ends up in the shop's till right away. The shop has to wait a day or two for cheques to clear and, considering that they tend to operate a bit hand-to-mouth [particularly at this time of year], that is not ideal for them.

How do you ask for a deal on a deal? Be nice. Just say something like "I really like this bike, and I want to get it, but is there anything else you can do for me?" They may not have a lot of budge space on price but, as MichaelW pointed out, they are always accessories. You'll NEED ahelmet. Maybe you can get them to sell you a $35 helmet for $25. You'll want bottle cages and water bottles. Maybe you can get them to throw those in.

You say the shop is giving you clipless pedals. I think that's great, but you'll need special shoes... maybe you can get them to sell you a $50 pair of shoes for $30... It all adds up.