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As for "midi instruments [you] may download", I assume you're referring to VST's. That's a little more complicated depending on what exactly you're doing. You'd probably need to mention the exact VST's you had in mind as depending on whether there is a native Linux version or whether you're trying to wrap a Windows only piece of software in a Wine translation layer like yabridge will determine exactly how that is accomplished. At the end of the day though, under Options -> Preferences -> Plug-ins -> VST (or LV2), you'll find the paths that will be searched by Reaper looking for virtual instruments and effects plugins at startup. Getting most of these types of things available under Reaper is "simply" a matter of dropping the correct files in one of those paths.
If you are running you own jackd command from the command line you probablt need https://github.com/jackaudio/a2jmidid