Hi Will,
welcome to LQ, and welcome to Linux
I neither use Ubuntu nor Vim, but I can give you some general hints.
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I am still not fully understanding about where packages get downloaded and installed by default, and why it matters.
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When you install a software package in Linux, the contents get distributed across the file system: executable files go in /bin or (mostly) /usr/bin, shared stuff such as media go in /usr/share, config files go in /etc, and so on. Normally you shouldn't have to worry about this, because programs find their stuff automatically -- that's why the mentioned default locations are used.
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I also downloaded the source folders and unzipped them to my home folder (as instructions on the vim-latex site/page, so I have those files there but not doing anything as far as I am aware.
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When you download a program as source code from the Internet, you have to compile it before you can use it! However, obtaining and compiling source code is not the normal way of installing software in Ubuntu. I bet that Ubuntu offers a vim-latex package (maybe the name is slightly different). Install that using the distro's package manager and you should be fine!