The first thing of course is to check you have the latest version of Project64 by visiting the official site - see Web Links.

Check if any of the plugins have been updated, this could make a large difference to your results. Keep an eye on any 3rd party plugins included with Project64 that you are using, which may be be updated independantly of Project64.

Aside from executable code (.exe and .dll files), Project64 uses several plain text files which are likely to be updated more frequently:

Project64.rds - the Project64 ROM Database Settings
Updates to this file could help you to get more games working by providing correct settings for each game, and by correcting mistakes in the settings for existing game entries. Updates may also assist you by improving user instructions in the Notes fields and correcting status designations. This is an important file to keep updated! See Web Links.

Project64.cdb - the Project64 Cheat Code Database
Updates to this file could add more cheat codes, correct existing cheat codes, remove cheat codes found to cause problems or not work, and improve notes for guidance. See Web Links.

Project64.rdi - the Project64 Rom Database Information
Updates to this file can provide extra information for games in the ROM Browser, such as Genre. Only a basic example file was included with Project64, so if you interested in using this feature, see if someone has published a suitable file. See Web Links.

Jabo.ini - This is used solely as a resource of all Jabo Video information requirements.
Updates to this file can provide extra information for games in the ROM Browser, such as Genre. Only a basic example file was included with Project64, so if you interested in using this feature, see if someone has published a suitable file. See Web Links.

These files are collectively know as the "INI files", "settings files" or "support files" (because they support the application, rather than support the user). You can check which versions of the files you are using at any time and visit the authors' homepages (to look for updates) by going Help > About INI files

"Offical" vs. "Unofficial" releases
A minority of the releases will be "Official" releases, which means they come from the authors or people nominated by them (probably the same people who produced the files that where included with Project64. Others releases are "Unofficial" (or, not official, they may not actually be marked "Unofficial"....), which means they could be from anyone.

People not familiar with the technical details of how these files work are encouraged to use Official releases as a means of quality assurance, but if you are confident then by all means use whatever you wish (or create your own).

A badly written file could render previously working game(s) unplayable, crash the emulator or just give incorrect feedback. It cannot do further damage to your system (e.g. they are just plain text and cannot carry viruses etc.). If in doubt, revert to the original files included with the emulator or the latest official ones (recommended). See Web Links for official file download locations.

Installing ini files
These are installed simply by downloading and extracting/copying it to the Project64 Legacy - 1.6.2 (Alpha) \Config folder, overwriting the file already there (if one is already there). It would be sensible to backup that original file (simply rename it before you begin) so that you can revert to it if you find something does not work afterwards.

Install updated plugins in the same way as you would add any plugin to Project64. Usually the updated plugin will overwrite the older one - if you don't want this to happen, rename either the old or new version, and check with the authors' documentation whether two versions can be used concurrently, or whether the old version needs to be uninstalled first (some can, some can't, it depends on how they use the Windows registry).

N.B. Make sure all files you install are designed for your version of Project64! Using older or newer versions could cause severe problems and must be avoided! Before installing any file, compare the version number with the one you are currently using by going Help > About INI Files. After updating you can go Help > About INI Files to confirm that the new file is being used.