I read this manga around 2009. The main character is a blonde boy whose father is "dead" and his mother dies shortly after I think. Anyway, he carries a large sword which can be powered up by placing these bead looking things in. On his journey, his friend is this attractive blonde girl. At one point, he finds his father, but then his father is killed when large stones fall on him. The manga revolves around the sword and the small stones you place in it. Any suggestions would be greatly appreciated.
I believe you are looking for Rave Master.
I have not read the manga, but the description really sounds like the story in its anime adaption.
Fifty years ago, the Demon Stone and RAVE (two powerful artifacts) are broken and scattered throughout the world. The story follows the journey of Haru Glory; during his travels he meets many new friends and allies, and also enemies known as the Daemon Card. He will have to use the powers given to him by RAVE to defeat the Daemon Card and find the other pieces of RAVE.
As for the death of the father:
However they stop as Elie is almost crushed by a blouder [sic!] and saved by Let who helps them escape. In the end, Gale [the protagonist’s father] falls down a hole and Haru tries to save him but they both become trapped, doomed to be crushed by the tower. However, after explaining to Haru the meaning of being a man and a father, Gale covers Haru’s body to protect him despite Haru’s pleas. After the tower collapes, Haru is horrified to find his father died protecting him. — Rave Master Wiki