Arcane Mark:
This spell allows you to inscribe your personal rune or mark, which can consist of no more than six characters. The writing can be visible or invisible. An arcane mark spell enables you to etch the rune upon any substance without harm to the material upon which it is placed. If an invisible mark is made, a detect magic spell causes it to glow and be visible, though not necessarily understandable.
See invisibility, true seeing, a gem of seeing, or a robe of eyes likewise allows the user to see an invisible arcane mark. A read magic spell reveals the words, if any. The mark cannot be dispelled, but it can be removed by the caster or by an erase spell.
If an arcane mark is placed on a living being, the effect gradually fades in about a month.
Arcane mark must be cast on an object prior to casting instant summons on the same object (see that spell description for details).
Runic Overload:
This spell charges magical runes to an explosive degree. If cast on a creature with magical runes on its body, such as a rune giant or a runescarred creature, it deals 1d6 points of sonic damage per caster level (maximum 20d6) to the target and stuns the target for 1 round. When the spell is cast in this way, it must overcome the target's spell resistance. A successful Will save halves the damage and negates the stun effect.
The spell can also be cast on other magical runes, such as those from arcane mark or explosive runes. In this case, the resulting explosion deals 1d8 points of sonic damage per 2 caster levels (maximum 10d8) to all creatures within a 5-foot radius. Creatures in the area that succeed at a Reflex save take half damage. This spell doesn't destroy runes; targeted runes continue to function normally. Mundane runes, such as ones in writing or runic tattoos, cannot be affected by this spell.
What would you rule if I were to place the Arcane Mark not on the floor next to the target, but on the target itself, then cast Runic Overload? Would the enemy then get a roll to evade a blast attached to their own body? This situation seems to be in favor of the first paragraph with "If cast on a creature with magical runes on its body", but paragraph 2 specifically speaks of Arcane Mark.
Also what if multiple Arcane Marks are attached to the target? Would only one mark explode?
I would say that a creature with an arcane mark inscribed on it would use the first set of rules, as if it were a rune giant or runescarred creature. 'Other magical runes' I believe means runes other than those on a creatures body.
In any event, the spell doesn't care how many runes are present, it does its damage one time, and doesn't destroy any runes. It basically has a very unique focus requirment: must have magic rune at the target