Confused !

After many years away from playing i have recently took up both the guitar and bass guitar again. This time though i want to do it properly and learn standard notation , theory etc.
Im learning from two different books and im stuggling to come to terms from changing between the bass clef and the treble clef. Surely piano players read both at the same time but i get confused changing from one to the other {bass guitar to normal guitar} when im practicing my sight reading . Any advice or will it just get easier with practice? Im sure theres a lot of you on here who also play normal guitar.
Just one other thing . Im learning bass from mel bays complete bass method. Ive been going along fine until i get to the bass parts sections with the intervals , appreggios and how they relate to chords. I just dont get it and the book never really explains how the theory links in . I was considering ditching the book and buying the hal leonard method reviewed on here but im worried there are gaps in my knowledge and ill be just wasting my time switching to another book.
Thanks in advance for any advice.