I've no doubt you've long since found the book you're looking for, but I'm almost certain it's the The Darkweaver Legacy quartet by Mark Robson, the first in the series being The Forging of the Sword.
From this review:
Calvyn, a teenage farmer, has gone out fishing for the day, and on his return journey, he aids kindly stranger Perdimonn, whose wagon has got stuck in the mud. Being the good Samaritan takes some time and effort, and leaves Calvyn with his face in the mud, after Perdimonn has miscalculated with his own particular way of doing things. The least Perdimonn can do is to offer the young lad a lift home...
The rune part of the magic is mentioned in a forum post by the author:
The magic in my world is actually a blend of other writers' ideas. I wanted to have something subtly different to anything I had seen, but that included some of the more traditional fantasy elements. Runes have been associated with magic in many different fantasy stories, including LOTR, but I didn't want my magic systems to rely on runes alone.
In keeping with other disciplines, I wanted there to be an element of mental discipline involved in magic. As the series moves on, you do get to learn more of the magical system, particularly in First Sword, where Calvyn spends some time at the academy in Terilla. The two elements - learning and mental discipline - are equally required to make magic. The idea of a basic mental exercise to fill your mind with the colour white drove me mad for weeks, as I actually tried to do it! Needless to say I did not succeed! I know that many others who have read the book have also tried it. :D
The mental element of magic is a derivative of the Eddings 'The Will and the Word'. However, I think it is dissimilar enough not to make people instantly compare the two forms.