I know that starting with ruby and sapphire, there are 6 "setless" basic energy that you get from theme decks, well 5 if you don't count the ones from ruby and sapphire considering that the theme decks from ruby and sapphire to emerald use energies with the ruby and sapphire symbol on them.
From Ruby and Sapphire onwards, there are 4 card frame designs. I mentioned that there are 6 separate copyright years on the basic energy. 2003 (this has the ruby and sapphire set symbol on them), 2005, 2007, 2010, 2011, and 2013.
The 2005 energies started with ex unseen forces
The 2007 energies started with diamond and pearl
The 2010 energies started with heartgold soulsilver
The 2011 energies started with black and white
The 2013 energies started with XY
You could do one of 2 things. Place the energies with the set they started with, or place them all in the end. If you do order the energies, they have to go in order of Grass, Fire, Water, Lightning, Psychic, Fighting, Darkness, Metal, then Fairy. That's pretty much the official order of how the energies should be organized. Another thing is that if you order it by collectors number, the Pokemon go first, then Trainer, then Energy.
If I had to guess:
Expedition base set to Skyridge theme decks use energies with the Expedition base set symbol on them.
Neo Genesis to Legendary Collection theme decks use energies with the Neo Genesis symbol on them.
Gym Challenge theme decks use energies with Gym Challenge symbol on them.
Gym Heroes theme decks use energies with Gym Heroes symbol on them.
Base set 2 and Team Rocket theme decks use energies with Base Set 2 symbol on them.
Base set to Fossil theme decks use energies with Base set symbol (no symbol) on them.
So if we continued this pattern of placing the energies in the set they were first introduced, the 2003 energies (has the ruby and sapphire symbol on it), should be place with ruby and sapphire.
The 2005 ones should be placed at the end of ex Unseen Forces.
The 2007 ones should be placed at the end of Diamond and Pearl.
The 2010 ones should be placed at the end of Heartgold Soulsilver.
The 2011 ones should be placed at the end of Black and White.
The 2013 ones should be placed at the end of XY.