My six week old baby has had running diarrhea poop a few times today and threw a few times, can i give him pedialyte?

Yes: If your child is still actively vomiting - offer your baby 1 tsp of pedialyte every 5-10 minutes. This is called Oral Rehydration Therapy and - tho a lot of work - is as good as an IV. Once no vomiting for 4 hours may proceed back to normal diet. Keep buttocks covered in vaseline to protect from the acid of diarrhea. Due to your child's age I would contact your MD for an appt tomorrow.