I too am teaching 6th grade science; however, we don't have the common core. Other than that we can collaborate and share ideas!
Coming from 3rd grade, you will notice quite a difference in the students abilities to work more independently. We had a teacher last year that had taught 1st grade so it was a big change for her though she found that she preferred elementary and went back.
Is your 6th grade at the elementary school, intermediate type or middle school? Do you have your own lab?
You mentioned pacing charts (and your question may be related to common core -- so I don't understand it), but don't you have specific state science standards that you have to cover in a specific grade? Or will you be going by the NGSS (new generation science standards)?
Just to suggest a couple sites that offer good resources just to get you started:
Keep your eyes open for the composition books that go on sale each summer so that you can use those for your science journals. I usually find these for 25-50 cents. We go through at least two journals each year.