For Ellie, when she squats I put a small measuring cup under her. It is a tight fit.
To get a sample from a pee pad, turn it over and let them pee then pour it into something. That is a table top sample though and there is too much chance for it to be contaminated with bacteria. If you can't get one, any vet should be able to take it (cystocentesis). That way the least amount of bacteria is introduced anyway.