Mama, it can be hard to feel like maybe something you've done or not done has caused your baby pain, but again, it could be very normal separation irritation and discharge and not a bacterial infection at all.
I saw that you mentioned on another thread that your doctor suggested circ. That tells me that your doctor isn't very informed about the intact penis and may have been prone to diagnose a bacterial infection because he is not used to seeing the normal developmental issues that can arise during separation. So I'm just saying, take the diagnosis with a grain of salt.
If the swelling is down you might consider holding off on the antibiotics for a day or so and see whether he truly needs them or whether in hindsight it was just separation irritation with some discharge.
Also you will need to keep an eye on the yeast because the antibiotics (esp. if he's taking oral antibiotics) may kill off the beneficial bacteria and actually make him more prone to yeast.
The penis, like the vagina, is self-cleaning -- there are beneficial bacteria and enzymes (lysozyme) with antibacterial activity inside the preputial space between the foreskin and the glans after separation occurs. Also, urine is sterile as it exits the body and really only a drop or so might remain behind. So unless he's rolling around naked in the dirt, he's really not going to get all that grubby inside his genitals in any way that requires a rigorous hygiene protocol or makes him more prone to bacterial infections.
Just as with women/girls, you need to be careful with washing so as not to upset the natural balance of bacteria and beneficial enzymes -- boys/intact men can get yeast infections from too much washing that upsets the pH levels and kills off beneficial bacteria, too. Soap can also cause irritation of the mucousal membranes of the glans and the inside of the foreskin. Think of your son's internal penis as being similar to the inside of your vagina and requiring the same kind of hygiene (i.e., plain water and very mild soap occasionally).
It's fine to encourage your son to retract as far as he can comfortably and swish in a bathtub of clean non-soapy water; but the best thing really is to think of your son's genitals just as you would your daughter's or your own and not think of the foreskin as a disease-prone ticking timebomb, which it really isn't!
I hope all is back to normal soon!