#1) I download the /modules and /skins folders. built into PhpStorm is an integration with GIT which is a revision control system. Before I download the /modules and /skins folders I go into ACP -> MODULES -> DEVELOPER -> DEVELOPER TOOLS -> TOOLS -> REBASE MODULES (and REBASE SKINS)
That takes all of the:
/modules/jrAudio-version-1.1.1
/modules/jrAudio-version-1.1.2
/modules/jrAudio-version-1.1.3
and deletes all but the currently in use version and puts that on:
/modules/jrAudio
So when I go to download it it downloads over the top of my local copy of /modules/jrAudio then GIT tells me that "you have changes to these files....." so I can see whats changed between my previous version and this version.
If you found that the piece of HTML you wanted to change was in the /templates folder of one of the modules but you wanted to change it, you'd use this method:
Docs: "Altering a Modules Template"
https://www.jamroom.net/the-jamroom-network/documentation/module-developer-guide/1051/altering-a-modules-template#override-a-modules-template
and copy the file to your skin, then make the alterations.
2) No. The template names are injected into the HTML when the page is displayed, if you download your skin you would not find that code anywhere.