Firstly
Apps/msm --> is is blueprint configs
libs/msm --> is for rollout configs
/etc/*msm --> is the legacy path.
Now when it comes to rollout config drop down, which shows in the blueprint tab of content page --> it will pick all the configs from /libs/msm/*. Here you cannot control the order of the elements in the dropdown unless by overlaying , which is not recommended.
When it comes to multiple rollout configs on the page ,depends on the order on how it is there is jcr:content . Order is as per the order in which rollout configs are added on the multifield.