EDIT: updated for Eden
To create any store:
First, you gotta load the mission in the editor, and place a civilian unit somewhere. Put it exactly where you want it, preferably inside a building; it will keep its original position and rotation. Just note that a desk will spawn in front of it, so make sure it's not too close to a wall.
Give it a name, depending on which type of store do you want: "GenStoreX", "GunStoreX", "VehStoreX". Replace the X with a number, it can be anything you want as long as it's unique for that type of store. Personally, I prefer to keep them ordered, so for Altis there are GenStore1 to 5, GunStore1 to 4, and VehStore1 to 4.
Then, you must set the Object Init of the unit to the following:
0 = [this] spawn A3W_fnc_setupStoreNPC
You can save the mission. Now, you will need to open mapConfig\storeOwners.sqf, and add entries in storeOwnerConfig and storeOwnerConfigAppearance.
The storeOwnerConfig entry should look like this:
["VehStoreX", -1, [], ["Boats", "Planes"]],
Change the X to your chosen number. The second and third parameters are obsolete values used for positioning in the past before Eden, keep them at -1 and []. The fourth parameter is an array to designate the buttons you want to exclude from that store, if there are no appropriate spawns. "Boats" and "Planes" will hide those buttons from the store menu.
Next, the storeOwnerConfigAppearance should look like this:
["VehStoreX", [["weapon", ""], ["uniform", "U_IG_Guerilla3_2"]]],
Change the X to your chosen number, and make sure all entries end with a comma except the last one. The weapon option is if you want your store NPC to wield a weapon, just put the classname in the empty spot. The second option is the uniform the NPC should wear, again just change the classname to your liking.
Pay attention to the commas; all entries should have one at the end, except the last one.
Last but not least, open up the editor again. You will need to set up markers where to spawn purchased objects. For general and gun stores, you need a marker named "GenStoreX_objSpawn" or "GunStoreX_objSpawn", again replacing the X'es. This should be placed on the road in front of the store building entrance.
For vehicles stores, there are: "VehStoreX_landSpawn" for land vehicles, "VehStoreX_seaSpawn" for boats and submarines, "VehStoreX_heliSpawn" for helicopters, and "VehStoreX_planeSpawn" for planes, again replacing the X'es. Make sure you set the planeSpawn rotation towards the direction for takeoff. landSpawn and heliSpawn are mandatory, you can omit seaSpawn if you have disabled boats, and planeSpawn if you disabled planes. Once those markers are placed, save the mission, copy-paste the SQM into your working directory if needed, and it should be good to go.