I guess you're probably trying to modify an official pack. Don't do it, theres a reason PFM tells you that you shouldn't. When you want to make a new mod, the first thing you do is set up a new pack. This means that if you screw up and do something which breaks the game, all you have to do to fix it is uninstall your mod.
Step 1: Add a new personal mod in PFM
File -> MyMods -> New. Enter the name and location that you want to store it. When it asks you to select data proceed to step 2
When you have a mod selected under MyMods, extracted tables automatically locate themselves in the mod directory which makes extracting multiple tables much faster
Step 2: Extract the files you want.
Open the official pack (probably data_rome2.pack) in PFM, and navigate to the file you want (I'll use data_rome2/db/kv_rules as an example). Right click -> extract -> extract selected. If you navigate to the folder you created for your mod, you will find a folder structure representing the location of the table in the pack (eg. <mod name>/db/kv_rules in my case) with a binary file inside cotaining the details of the table.
Step 3: Import the files into your mod
File -> MyMods -> Select your mod
Files -> Add -> File(s)
Navigate to the binary files you extracted and add them. You can use the directory option to add a group of tables at once, but be careful to keep the structure the same and not accidentally add another level. Individual Files is safer
Step 4: Make your changes
Step 5: Install your mod
PFM has a great feature where it can manage the user.script.txt entries and add your mod.pack to the Rome2 data folder for you.
File -> MyMods -> Install ____ (depending on which of your mods you have selected)