I should really do an actual write-up and get it stickied in the FAQ up top one of these years.
Basically, what is required is more than one RSE cart and more than one GBA. From my experience, you can have 20 Secret Base locations at any one time, and after that a new base will replace the oldest one. For those that don't know, when one cart that has a Secret Base mixes records with another cart that has a Secret Base, that location will show up on the other cart, as long as they don't share the same location. Then, once per day (or I should say once per mixing records) you can visit the Secret Base location of the other cart and battle the Pokemon that the other cart had in its party when it mixed records.
The very first thing I do is put together my EV Pokemon that I will be placing in the Secret Bases. It is VERY helpful if you have access to FRLG, but not required. Personally, I choose Pokemon that not only provide 3 EV points in each category, but can be obtain at the lowest level possible. Here is what I use:
HP - Lv5 Clefable (use Moon Stone on Lv5 Clefairy, traded from FRLG)
Atk - Lv14 Shiftry (use Moon Stone on Lv14 Nuzleaf)
Def - Lv25 Golem (trade Graveler to evolve)
SAtk - Lv10 Beautifly (evolve Wurmple)
SDef - Lv10 Dustox (evolve Wurmple)
Spd - Lv5 Raichu (use Thunderstone on Lv5 (or lower) Pikachu, traded from FRLG)
You can catch Pikachu in Emerald at the Safari Zone, but the levels are higher and you would have to breed Pichu and then evolve through Happiness to get Pikachu. Again, trading from FRLG is preferred. I would then take the Pokemon to the Move Deleter in Lilycove and remove any offensive move that Pokemon had, giving myself 6 Pokemon punching bags for which to play with. I would suggest leaving the Pokemon with a worthless defensive move like Tail Whip at all possible. Tail Whip lowers your Pokemon's Def, but since the EV Pokemon has no attack moves, it doesn't matter anyway.
Simple, eh? Is it, but I won't lie and say that it doesn't take some time. Personally, what I would do is breed Mudkip (Ice Beam, Protect, Surf, Toxic), Taillow (Aerial Ace, Facade, Quick Attack, Steel Wing), and Ralts (Calm Mind, Hypnosis, Psychic, Thunderbolt) in Emerald to get the proper Natures and then walk with the egg until it was just ready to hatch. I would then store them in the PC, so I had a box full of eggs of each. I would then get a Wailmer (Dive, Surf, Rock Smash, Waterfall) and Tropius (Cut, Flash, Fly, Strength) to use as HM slaves as they learn all 8 between them. Then I would start a new game on my Ruby cart, select Treecko so May would select the craptacular Torchic, catch 4 Pokemon near Oldale, and then trade them for the 3 eggs and 2 HM slaves.
After walking for about 20 steps my eggs would hatch, and I would be ready to go. I chose Taillow over a more superior Flying-type (i.e. Salamence) mainly because Taillow levels up quickly and helps a lot at getting through the Petalburg Woods very easily and taking out the second gym faster than Marshtomp. I also have earmarked locations of all the good items (i.e. TMs, Everstone, etc) throughout the game so I can collect them and also transfer them to my Emerald. Anyway, after defeating Wattson, you are able to head north on Route 111, where you get Secret Power. It is at this point where you are able to create a Secret Base. The first few runs don't usually take long, and I will rarely even use Ralts. I will find a suitable location and stop.
At this point I would place the EV Pokemon that I will be using for that base (i.e 6 Clefairy) in my party on Emerald, trade across the Pokemon I had in Ruby (along with the collected items) and then mix records. Now my Emerald has a Secret Base location with 6 Pokemon with 3 EV points each. Lather, rinse, repeat.
My strategy for the bases is quite simple. 3 bases of each stat, one base with one EV Pokemon of each stat, and then one final base with 6 Lv100 Chansey. I would also map out the locations and keep the like bases as close together as possible to help cut down on the time it took to EV train.
One VERY helpful item in the EV training process is the Macho Brace. This held item will DOUBLE the amount of EVs your Pokemon earns from battle. So instead of getting 3 EV points per battle, it will now get 6 points. Something even more helpful is the rare Pokerus. It is a virus that, just like the Macho Brace, will double the EV points earned, allowing your Pokemon to earn 12 EV points for each battle. Pokerus is hard to get though, but sometimes (as is the case with me) you will find a friend that has it and will be willing, not to mention honest, to take your cart and give you an infected Pokemon. If you have access to DPP and can Wi-Fi, that makes it even easier.
So, with 3 EV bases, the Macho Brace, and the Pokerus, your target Pokemon can earn 216 EV points in a matter of minutes. From here you can get an additional 12 EV points from the 19th base, and then finish up EV training in the natural areas in the game that are full of certain Pokemon. Again, here is where I go:
HP - Marill, Petalburg City (Surf) - appears 100% of the time
Atk - Carvanha/Sharpedo, Route 118 (Super Rod) - 100% (also great time to search for Feebas)
Def - Torkoal/Geodude/Graveler, Magma Hideout - 100%
SAtk - Spinda/Slugma, Route 113 - 95%
SDef - Swablu/Lotad/Lombre, Route 114 - 90%
Spd - Golbat, Surf at Meteor Falls - 90%
Don't fret if you don't have Pokerus though, it will only take an extra day to get where you want to be. To be honest, there are not a lot of Pokemon that really need max EVs in a stat anyway. That is where the final handy item comes into play - Exp Share. Tag along 5 other Pokemon with your target Pokemon, give them all an Exp Share, and they will still at least earn 3 EV points per battle, or 6 if they too have Pokerus.
To sum up, while it does take time to set up, for me it is a godsend since I can EV train daily in just a few minutes. You just cannot beat that.