You may need someone to help out. Do it during the day while she is sleepy and a bit easier to control. Put your hand under her while she is still in the pouch and then let her settle down in your hand while still in the pouch. Once she quiets a bit Put your other hand over her as you lift her out. You hold her very gently, but firmly, so in spite of the crabbing and fussing she doesn't wiggle out of your hands, and have someone else very gently wipe her bottom with a damp washcloth. That is the way I would do it anyway.
The loose stools are most likely caused by the stress of leaving her parents and home, and will become normal in a day or two. Be sure she is getting plenty of water so that dehydration doesn't become a problem. You can add Pedialyte to her water to replenish electrolytes lost from the diarrhea. Be sure she is on a good glider diet. There are several
here to choose from. Many people use the BML diet because it makes getting the vitamins and calcium in the glider easier, and they do very well on it. There is also a baby glider version of this diet.
It is a good idea to take your new glider to the vet for a check up anyway, so you might want to do that, just to be safe.
Hope this helps.