I used to underline the Quran with pencils when I'm studying in Religious Class during my childhood. But now I refrain doing that because I tried memorizing Quran. I also wash my mouth, shower, performing ablution, wearing perfume with clean clothes, and burning fragrants when reading Quran and memorizing it in order to respect the words of Allah. But I think, its enough performing ablution and washing mouth when you want to read Quran. We can't touch it without ablution. After reading it place it in highest place. If for English translation, I think no problem, it's just a translation however we Muslims use to respect and treat knowledge in the highest manner. All of them came from G-d.

And G-d knows the best...

It sounds like if you are reading an Arabic Quran, you should make sure you're clean and not distracted--though I'm not sure if marking it is considered permissible. It also sounds like being ritually clean isn't necessary when reading a translation of the meaning of the Quran--though one should respect it.

I do understand--and largely agree with--the position that certain objects should be treated with dignity and respect, because our care for these things indicate our care for the God who gave them.