My favorite way to meditate/study the Bible is simple.

Read and reflect several times on the particular book of the Bible.

Take out a legal pad. 

Grab a cool pen.

Bombard the text with questions, connections, musings, etc.

Put my most significant thoughts in my two study Bibles.  One for each one of my sons when I kick the proverbial bucket.

Meditate throughout the day on at least one overall lesson.  Possibly meditate and then commit to memory a verse or two.