Zion Clark does have a penis as well as a bladder and urethra and so Zion Clark does use the toilet to urinate, just as any other male would.
Although when peeing, Zion Clark sits down from his wheelchair.
Zion Clark may sometimes use a tube to urinate, but if he wants to, he can use a toilet.
Although Zion Clark was born without legs, he does still have all of his necessary internal organs, which include a bladder as well as urethra, which allows him to urinate or pee as normal.
The method that Zion Clark uses to pee or urinate is to sit on the toilet from his wheelchair.
Zion Clark has a condition that is called Caudal Regression Syndrome, which is a rare disorder that caused Zion Clark to be born without legs, but the Caudal Regression Syndrome does not prevent Zion Clark from peeing or urinating in a toilet as he normally would.