I am making a new RPG system loosely based on "Warrior, Rogue & Mage" and "Resolute, Adventurer & Genius", but with quite a few modifications. One of them is that the skills are split into "military" and "civilian". The xp points are awarded equally to all members of the players party after each adventure or episode of the campaign. Each adventure has a reward in "military" xp points and "civilian" xp points depending on the scenario and the way the players handle the adventure. As you have guessed, "military" xp points can be used only to increase "military" skills and "civilian" xp points can be spent only on "civilian" skills.
What do you think about this?

It is generally a good idea to split combat stats from non-combat stats, if you have a turn based combat system. That's because once combat goes down you will use combat stats several times. It's very hard to balance that against singular checks out of combat.

Of course, if you do not have a turn based combat system, that argument does not applay.

Runequest/Basic Roleplaying takes this to the logical limit of making improvements with a skill totally based on using (or training) exactly that skill. There are no general improvements from adventuring. That works fine, but it is easy to track given the system and the character sheet arrangment.

I don't see the benefit in separating skills into just two buckets. Aside from pure combat skills like swinging a sword there doesn't seem like there is a really clear division. There is a fair degree of overlap between military and civilian skills, e.g. leadership and organizational skills and craft skills like smithing, leatherworking, and carpentry would be common to both military and civilian professions. Archery would be common to both hunting and soldiering. So is hunting a military skill?

Figuring out which part of the adventure was which and tracking it adds complication for what seems like a pretty minimal benefit.

As a GM I talk with the players about how they justify their improvements and find this works better for me than a detailed, hard and fast rule restricting what can be improved. Most players actually seem to like tying their character's improvements to what their PC did in play or what they envision their PC doing between adventures.

As with anything YMMV.

My heart breaker used the same 3 classes with a rough Combat/skills/magic spit.

However, with XP you need 10 XP to gain a level you gain XP for overcoming obstacles personal or plot driven (talked about this before elsewhere). XP awards are generally proportional to risk. So it roughly takes a 5th level guy as long to gain 10 XP as it takes a 1st level guy.

Once you level you spend XP from the pool of options from HP, Defence, Attack etc. Each class gets a set of freebies as they level their other options depend on their archetype which sets skills classes, their class etc.
You can only buy 1 rank in 1 thing per level.

So a warrior with the soldier kit goes from level 1 to level 2. They get a free HP and a free +1 attack.
They can spend 10 points on Skills (2 points each from the Military list), HP (1 each), combat styles (1 rank per point) , Armour mastery, or indeed save them to buy a school of magic at 30 points each.
The result is a level and class model with an imbedded skills system. As you can only buy 1 rank in a thing as you level the max rank you have in anything is your level.

It is probably highly exploitable mathematically but that hasn't really come up.

Anyway a variable is for the PCs to select what they want to buy with their ten points the level before so at first level you select what to spend your 10 point on when you reach 2nd and that then clicks in when you amass 10XP. You can change your mind but at a 2:1 penalty. So drop a 2 point skill for an extra HP in this example.

The system is rule lite (I want to keep "player manual" under 20 pages if I can), classless and intended for absolute beginners to Pen&Paper RPG's but it must have enough complexity to keep a more experienced player interested in playing it. Also it must be played with six sided dices only. But I don't want to give too much power to GM and I don't want fight oriented power players or magic oriented power players to drag the other characters in dire situations. Player will be crafting their own magic items and the wizards will craft their own personal spells.

You know, you could handle the two types of skills utterly differently.

One could be use-based (like BRP), one could be XP-based. Or whatever other system you want.