Usually, the standard is to wait 4-6 months to query the same agent with a new ms, unless they have invited you to send them something else. The thinking is that your writing can grow in a few months time. For PBs, it's a good idea to have several strong mss, as an agent will probably want to read more than one before offering. (My agent requested two more mss, as well as an illustration revise before offering on our second phone call) You should query with your strongest ms. It's a good idea to see if there is a common reason in the rejections and you can revise before sending to more agents. If the newer ms is the stronger one, then you can lead with it. If you think you have several strong mss, query with one but you can mention you have other work available for them to review if they are interested.
It's been a long time since I was querying, so I may be out of touch with common query practices.