Alternator wiring
 

I have a 5.3 truck engine with the factory positive battery cable connected on the drivers side. Now with that cable it's connected to the alternator power stud on the back, then the cable runs to the starter like it did from the factory. I have my battery mounted in the trunk with the cable running down the passenger side and directly to the starter. Now my question is will my battery still be able to get charged since both wires meet at the starter or not?

Yes, it will charge just fine.