That is precisely how the default battle system works. To do what you're asking requires no changes to the system at all.
The default "Attack" action is a general physical attack that is modified by the character's Strength and Attack power, and the enemy's physical defense.
"Skills" can have physical and/or elemental properties (such as "Magic," "Fire," or "vs. Undead") These properties are determined on a skill to skill basis. In addition to the elemental tag, skills can be modified by most any attributes (Strength, Dexterity, Agility or Intelligence) or any combination of them that you want. They can also use an SP cost determined by you.
All of this information is explained further in RMXP's included help file. I suggest reading the "Battle Formulas" section.