To add new items to the Matter Registry, just add their unlocalized name or Ore Dictionary name and the amount of matter it requires in the matter registry > new items (no whitespaces).
This is different from changing already registered items by Matter Overdrive or other mods. To change existing items, check below.

"matter registry" {

   "new items" {

If the unlocalized name contains characters that are not alphanumeric and are not “-“, “.” or “_”, the name must be surrounded in quotes like I:”tile.projectred.exploration.stone|2″=1.
Note that the exact name will be used before the dictionary name. If you have a specific amount registered to jungle planks, then the ore dictionary for wood won’t be used.

You can also add items in-game by using the Matter Registry command while holding the desired item. Using that command will also add the item to the config automatically.

A good way to find the names is to use the minecraft language file

Changing the matter of existing items is similar to adding new items. The only difference is that instead of adding the items in the “new items” category of the config, you must add them to the “item overrides” category. This is used to add new values to items already registered by Matter Overdrive or other mods.

Blacklisting an item is much easier than adding one. Just add their un-localized name or Ore Dictionary name in the matter “registry > blacklist” category without commas.
Blacklisting items will prevent the automatic calculation of recipes containing that item. This is a great way to prevent certain items (and subsequent items crafted with it) from being replicated. For example, dilithium crystals are blacklisted.

"matter registry" {

   S:blacklist <