A pop-up flash has barely enough power to work indoors of a residential space; in larger rooms, professional photographers have practical reasons why they carry separate large flashguns. The Puffer, whilst making the light slightly less harsh and therefore more pleasing, does it so at the expense of chewing the power even further down.

So, your gear is quite stressed to get those pictures. To get the best odds, I'd probably jack ISO as high as you're ready to accept resulting noise (this is something you'll have to test out beforehand yourself, shooting same scene at different ISOs and comparing the results to see what's the noise level of each ISO - "getting to know" your camera). To get the best efficiency from flash, I'd set the exposure mode to M, and shutter speed to max sync speed of the camera (1/200s for the D3000) or slower (for non-action photos). I'd start off with aperture at around f/4, adjusting the F-number lower when the pictures seem to be underexposed or higher if there seems to be plenty of light and I'm having trouble getting focus nailed. There's almost never enough light indoors to worry about overexposure :)

The reason you're getting yellowish tones is that the light coming from your flash has different tone (matched with sunlight) than the "warm" lighting used indoors, and your camera assumes flash being the "correct" tone. You could tell the camera to use white balance matching the indoors lighting ("incandescent"), but then areas lit by flash would seem bluish. The real solution here would be to adjust the light of flash to match the ambient lighting by inserting an appropriately colored transparency in front of it (this is called "gelling"). CTO (or CTS) gels are the basic accessories for indoors flash photography.