While at home, ill set up anything, cups, shoes, anything 4 and a quarter inches.... and chip at it, keeps the short game sharp and it doesn't hurt anything... as long as your pretty careful... but I only like to use real golf balls, the difference in reaction from a whiffle type ball and the real thing is so substantualy diffrent that you loose the feel of how the chip shots are going to react, and feel is the name of the game with your short game... thats all you would be doing indoors anyway, not like your going to hit full shots.
if you have a yard, I recommend the "almost golf" foam balls for full shot practice, they are wonderful for mimicking the flight of a real ball while only going i think a fourth of the distance.