3 yr old cat and 6 wk old puppy...?

Quick question... I just brought home my 6 wk old doberman puppy today... and my cat (who is already WAY shy, timid when around strangers) is simply acting crazy! She runs and hides, under beds usually, and won't go to any of her 'usual' spots (IE looking out the door, her favorite chair..ect). Skittles (the cat) was bottle fed from 3 wks old, and has never interacted with any other animals (except my parrot, who she's been around since she was a kitty)... do you think she'll ever warm up to the puppy?! As the puppy grows, it will be spending more time outside, and Skittles is never allowed out.. so I'm hoping she'll learn that the puppy isn't taking over her turf? I refuse to let the pup in 'her' room... (where all the kittys toys ect are.) but are there any other things I may could do to ease the tension/stress of my kitty? The puppy LOVES my outdoor cat, so I know she'd love Skittles too... :( I'm really worried about my indoor baby, she is spoiled and I adore her. I don't want to hurt her or make her feel unloved! Any tips? PLEASE?