He will not receive time credit on his warrant case unless that state / county puts a detainer on him - which will hold him when he is released in Virginia.
As far as the new case, if the police reasonably believe that they smell marijuana, this creates probable cause to detain and search. You do not say what kind of drugs were found, but it sounds like your boyfriend has a good chance of getting off of the charge. He is not the driver. He is not in control of the vehicle. The drugs are not in plain sight. The drugs are not in his view. The drugs are inside the bag of another person in the car. The other person's name is on the bag. One potential issue is whether your boyfriend had a bag in the trunk, too. But, this is a minor link.
Other than being a passenger in a car that has drugs in the trunk, there is nothing to connect your boyfriend to the drugs in the truck. There is nothing to show he had access to the trunk because he was not the driver and did not have the key. (Unless he had a bag in the trunk.) There is nothing to show that he even knew that the other party had drugs.
If your boyfriend is able (and could pass), he could take a drug test (within 3 days generally unless it is a hair follicle test) to demonstrate that he was not using the drugs that were found. (This would be between he and his attorney, and not for the prosecutor to know unless it came back clean and his lawyer decided to share the information.)