am i creating an alpha dog?

my 8 week old puppy (adopted 2 days ago) is learning to eliminate on newspaper, as she hasn't had her shots and can't go outside. she is fine with the crate, but she does attempt (though much less now) to poo and pee elsewhere. i've been following her around to grab her when she squats down and take her to the appropriate place. also, i replace her chewing with toys everytime she tries to chew on furniture. however, i feel that i might be creating a situation where the dog is taking lead - as i follow it around.

i am at home all the time (writer) and have plenty of time to train and play - which i do. should i be keeping her in a play pen? or is it ok to follow her around to catch every single mistake she makes? need help. thanks.