The 2 things you need to stick to: a single element per team, AND a collection of single element weapons which are the same element as your himes/ soul. The way they work is the weapons possess skills that give stat buffs only to the element of said weapon, therefore both conditions are same element.
Eidolons are... slightly more flexible. The general rule of thumb is that your main eidolon is either your team's element, or their eidolon effect buffs your team's element. For sub eidolons, you generally want to go for stats. Atk is preferred. The only exceptions are if they have really good eidolon effects, such as Vine, if you don't have 50% def break.
Use the R eidolons as XP fodder. Outside of Vine (and maybe, but less so Anzu and Yamata no Orochi), all SR and below eidolons are safely fodder.