I wouldn't worry about her too much. She is probably just very nervous from all of the noises in the petstore, and being in a house is a big change.
When you offer her treats, try something fun, like a piece of dried fruit, or even fresh. Mine always loved bananas and apples. Sunflower seeds (in the shell) are a special treat, as is a little hard boiled egg. Now that the holidays are approaching, watch the stores for specials on nuts (walnuts, pecans, acorns, etc.) and buy a bit extra. You can keep them in the freezer, and only take out one or two at a time. It is a toy and a treat all in one. Watch the amounts on these, though, as they are very high in protein, and this can be a bad thing. Several dried cereals are fine. You could also try a cooked chicken leg bone. While it is not a good idea to give these to other pets (dogs, cats, etc.) rats grind them up fine with their teeth, and will not come to harm with them. All of my rats have always loved them, even the rescues. I have read on several websites that corn is not a good idea, as it generally contains preservatives and chemicals that rats can be sensitive to. Some say it is fine.
Yogurt drops are great, but sometimes pricey.
Make sure she knows where the food and water are. Also, watch to make sure that she is not feeling threatened by the larger rat. Sometimes, when a rat is particularly shy, they would rather just hide than face a new friend, even if it means eating a little less. You might try two food dishes, placing one right by where she likes to hide. Same with the water.
I would continue to pick her up and pet her. Talk to her in a gentle warm voice, while holding her close against your body, so she feels secure and protected. Offer her special treats just for "putting up with" you holding her. It is very easy for a scared rat to go from being shy and nervous to terrfied when they have no physical contact. I would continue to pick her up and hold her at least once a day.
Give her a few pieces of paper towel to shred and build a nest with. If she feels that she is the one making a home, she will settle in faster. Cardboard tubes are great for chewing, also. Depending upon how much cage space you have, cut a door in a shoe box and place it upside down on the floor(make sure there are no staples or silica gel packets in it first).
Everytime you go past the cage within hearing range, say her name. It will get her used to your voice. Even if you are not going to be picking her up, stand next to the cage for a moment, so she can become accustomed to your smell.
Eventually the marking will stop, I would think. Some rats, however, continue to do it. One of my males did right off whenever I took him out of his cage. It is a way for them to mark something as being "theirs". So I guess, in a way, we should feel honored that they claim us, right? "Oh, goody, here's my human and I'm going to poop on her!!"
I ran a rescue for a time, as well as had a large number of my own rats. Unfortunately, my son has developed allergies to everything with hair. We also lost our two old men, Cuddles and Snuggles. If you have any questions, please feel free to ask. If I cannot help you, I'll try to find you a link that does.
You are more likely to get a hold of me through email, though, as I only stop here periodically.
