Words

Get the Jap Pokemon Rom and the translation file you would like to use, extract them into the same folder.

This is an example using the 'Ruby' patch:
With the Pokemon rom file, mines is called 'pokemonruby (J).gba,' rename it to 'pokemonruby.gba'

With the Ruby translation patch called 'LARZ_95.IPS,' rename it to 'pokemonruby.ips'

In other words, both the Rom File and Patch file MUST be the same name.

Proceed by MAKING sure you have the latest Visualboy Advance 1.31 and use that to open 'pokemonruby.gba.' The new Visualboy Advance 1.31 automatically applies the IPS patch file given that it is the same name as the Rom File.
Navigation: Home>How to Patch Pokemon Ruby / Sapphire
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How to Patch Pokemon Ruby / Sapphire
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Diagram

Rom:  pokemonruby (J).gba       rename ===>     pokemonruby.gba
Patch:  LARZ_95.IPS     rename===>       pokemonruby.ips
Both in Same Folder
Use Visual Boy Advance 1.31 to open the pokemonruby.gba
Should work.
Since everyone learns different ways, I made it into 2 different explanation. One in WORDS  and one in DIAGRAM. Both tell you the same.