Assuming you've looked into how to add an existing object to the build menu, you'll need to remember that the files you modified must have the same exact directory structure as you found them originally. For example, if you modified an MBIN file inside a directory called /METADATA/REALITY/TABLES/, you must preserve the same directory structure. You don't need to copy other files in the same directories if you didn't modify them, as this will only increase the size of your mod.
If you copied the directory into another folder such as "MY MOD", your directory will be /MYMOD/METADATA/REALITY/TABLES/ and so on. However, make sure that MYMOD doesn't contain ANY special characters (e.g. ( ) or [ ]), otherwise NMS Modding Station will NOT pack the mod correctly. This is due to an aspect of PSARCTool built into Modding Station, and applies whether you're using PSARCTool.exe or NMS Modding Station to pack your mods.
Packing Mods Edit
To create your own PSARC archive, or .pak file, configure a projects folder path in NMS Modding Station via the top left Setup option, Set Path to Your Mod Projects folder/directory.
If you don't have such a folder/directory yet, create one called something like \My Mod Projects\. Within this folder you would place \MYMOD\[duplicated game directory structure].
Once you have the directory structure sorted out and your recompiled MBINs in the appropriate folders (e.g. BASEBUILDINGTABLE.MBIN in \METADATA\REALITY\TABLES), double click MYMOD folder in the Project tab of NMS Modding Station, right click within the MYMOD folder, select Pack Mod, and you'll find yourself with a .pak called MYMOD.pak. Feel free to name this file anything you like, but the general convention is _MOD.MYNAME.MYMOD.pak.
Running Mods Edit
As of the Foundation Update, all mods are now run from a new MODS folder that you make in your default PCBANKS directory. Simply pop the ENABLEMODS.txt in the PCBANKS directory in a backup folder somewhere, then place your .pak file inside the MODS folder and run the game to check that your mod is working as intended!
It's important to note that mods are run in alphanumerical order, so the numbers/letters you use for your mod's filename will affect load order (e.g. 'a' would load first between filenames only with letters, and 'z' would load last, potentially overriding changes from earlier mods if they use the same files). Alongside that, as a simple matter of course, mods that use the same files will be overrode by the last mod to be loaded.
Considering this, if you don't wish to test for mod conflicts/issues, simply notify users in your mod description of what files you've modified and that this may create conflicts/issues with other mods that have changed the same files.