water bath processing for jam
You can process in two batches. Occasionally a jar may not seal properly, you can reprocess it with in 24 hours, according to freshpreserving.com/fresh-preserving-solver. 


  What happens if a seal fails?
  
  Use food or refrigerate immediately. Only If the food was properly processed the first time, you may correct and reprocess if done within 24 hours. If an ingredient was left out, an ingredient was added, the wrong processing method was used, or the food was not processed long enough, you only have TWO hours to reprocess correctly.


This would apply to your situation as well. I would fill the jars and get them ready to place in the water bath, then process as soon as the first batch is done. They should still be quite warm which will help insure good vacuum and seal.