I tried taking on one with a yellow aura, and didn't make it very far.
I also have no idea how many points to invest in any skills. How do I get detailed information on what a skill point will do? Right now I'm getting things like "Next level: +ATK!" which isn't particularly helpful.
For the time being,
this Skill Sim is your best resource. I want to try and get the missing data when I get the chance.
My Runemaster for example, do I put all her points into one element? Or is 5 in each good? Or do I split it between 2?
My suggestion is to pick two Elements (ideally, Volt and Ice but it's your choice) and unlock their respective Damage spell and then stop leveling them. The gain in Damage per point isn't that big of a deal. Instead, I'd go and level other things to flesh out your pre-requisites.
So, for instance, a sample Level 15 (17 points) setup:
Proficiency 1/1
Ice Rune 1/6 -> Ice Lance 2/10
Volt Rune 1/6 -> Lightning Rune 2/10
Runic Gleam 3/6
TP Boost 6/8
1 point free
So I went dual-type Volt and Ice here and stopped at 2 points for their respective Runes since that's their pre-reqs. Ice gives you a nice ranged spell (@75% Damage) for nuking their back row and Volt gets you a line target with the best damage of the first Tier (@107% Damage).
Runic Gleam was stopped at 3/6 so the TP Cost does not increase (8 TP, jumps to 12) and three turns of +37% Damage is worth the 8 TP cost. TP Boost is stopped at 6/8 since it's 130% and I like the round number; realistically, you could stop at 5/8 since that's when it slows down (last three points are only +3% each, for instance).
16-19 can be used to max out Runic Gleam and TP Boost or, again, you can hold them; my recommendation is to sit on them but it's up to you. So, let's go to Level 25 (27 Points):
Proficiency 1/1 -> Expertise 1/1
Ice Rune 1/6 -> Ice Lance 2/10 -> Glacier Rune 2/8
Volt Rune 1/6 -> Lightning Rune 2/10 -> Storm Rune 2/8
Runic Gleam 3/6 -> Runic Shield 2/4 -> Runic Guidance 2/6
TP Boost 6/8
Free Energy 1/6
Runic Flare 1/10
Same logic as before. We're filling out spells to fulfill pre-reqs. Glacier Rune and Storm Rune fulfill similar roles so you'll basically just use them depending on the weakness. Glacier Rune is a random all-target spell and Storm Rune flat out replaces Ice Lance for your ranged single target damage. Runic Shield is there as a pre-req requirement (not that it's bad, mind you, just don't need more yet) and Runic Guidance is free bonus damage on targets with a weakness. Runic Flare is just a nice flat damage passive. For 26-40, I'd just recommend maxing out Runic Guidance and getting Runic Flare at least to 5/10 (116%, maxes at 125% so up to you if that last stretch of 9% Damage is worth 5 more skill points).
I can do a 40 and end-game one if you want, just feel like this is enough for the general philosophy of it all. Of course, since Resting is only -2 Levels, this isn't THAT big of a deal at all.
tl;dr: Few points in many skills > Many points in few skills. If you do pump a skill, take it to half for ~65% of the effect and then debate if the last ~35% bonus is worth it. If all else fails, don't worry since you can rest for so cheap.
When can you start subclassing? Also what level do most people beat the game at, and I'm guessing there's a new game+?
In the middle of the 3rd Dungeon.