Keep the new kitten separate until both are current on their vaccinations, test negative for Felv/FIV (feline leukemia and immunodeficiency virus), and get a clean bill of health from your vet.
Kittens that young usually have no need to be separated once they are vaccinated and deemed healthy. They'll spit and hiss at each other a little in the beginning, but they are too young to worry about harming each other. I highly recommend you spay and neuter both BEFORE they are old enough to reproduce, and secondly, that you get a female kitten for your male kitten. Males always take care of their females, trust me. My female beats the crap out of my big boy, then my boy spoons her and grooms her and loves her. My big male cat was incredibly lonely and depressed before I brought in my little female. She has honestly brought him back to life, and now he plays with her like a kitten (he is now 5, she is now 1.5 yrs old) Both are rescues, and both are spayed and neutered.
Regarding bowls and litterboxes: You should keep 2 litterboxes available for them. Get them used to the covered litterboxes, so they don't end up kicking the litter all over hell and back. I highly recommend using feline Pine or other brand of pine litter. It is the best! I'm allergic to pine, but I deal with my miserable allergies because it truly is the best litter out there.
I keep one large water bowl available, and I feed my cats separately in 2 smaller, separate bowls. Just feed one by the water dish and the other one teach to go into a carrier to be fed. This can be accomplished by putting one of the kittens into the carrier and shutting the carrier door every time you feed her. I have always done it this way, because this allows me to measure out their food, to see how much each cat is eating and if there is a problem, and to prevent one cat from gorging on the other's food and also getting fat while the other cat goes hungry. My little female now runs into her crate to be fed. I highly recommend you measure the amount of food you give them once they are around the 6 or 7 month mark. They will be spayed/neutered before then (spay and neuter by 4 months of age latest to be sure of preventing pregnancy) and will have the tendency to gain weight and become overweight. I use only metal bowls, since plastic bowls can cause feline acne. I also now feed my big 14-15 lb male and 9.5 lb female 1/4 c twice daily each of Innova cat kitten and cat food (not EVO, it's too high in protein). I give them 15 minutes to eat, take away any remaining food till supper, then give them 15 minutes again to eat their supper. They are different weights yet both receive the same amounts yet my female always leaves some left over. For a young kitten, give them as much as they want to eat and give them 3 separate opportunities to eat. Again, teach one to eat in the carrier. I also give my kitties a small tsp of soft food at night as a treat.