We have a 5 month old Shih Poo and she is gaining weight quite nicely since we adopted her. Our problem is we are not certain if we are feeding her too much. We currently are feeding her 3 times a day but think we need to take it to twice a day. How much is recommended per feeding? She currently weighs about 5 pounds. She poops a lot and we wonder if she is being fed too much. Plus it still is not as hard as we think it should be. Should it be soft, it makes it difficult for immediate clean up. She does literally clean the bowl at each feeding.

Twice a day should be plenty at this age. Appetite does not always indicate the appropriate amount. Keeping the dog lean will increase their life span and health. The amounts depend on your dog's activity level and weight. Consider trying the same amount at feeding time, but reduce to twice a day. If feeding ANY people food, remove this immediately. If the poop does not firm up after this, try changing the kibble (gradually!). There are many on the market that are produced for smaller and firmer waste. Personally I use Ultra by Nutro, an all natural holistic dry kibble and I've found it provided much firmer waste for my dog who previously had very loose stools due to her nervous tendencies.
Talk to your vet if you are unsure about the appropriateness of her current weight. Also check this website http://www.longliveyourdog.com/twoplus/RateYourDog.aspx

We currently use Nutro Natural Choice, do you think it would be advantageous for us to change to the Ultra brand to firm up her poop?

It definitely made a difference for me. I went from Science Diet puppy to Ultra puppy and saw a decrease in quantity and an increase in firmness. My dog is now on the adult version since about 8 months.