Samantha,
In answer to your question about how to do the vocabulary sheets within DITHR, I first agree that from what you've shared (with a child reading at the 5th-6th grade level), there is no need to do further phonics.

Kiddos who do not have good decoding skills typically cannot get past a 4th grade reading level (as by then their sight word memorization word bank fills up and then the fact that they cannot decode reveals itself).
It isn't uncommon for kiddos to guess at words once they start reading at a higher-level and at a faster speed. Guessing is easier than decoding!

In order to help her, I would have her read at least several pages aloud to you each day from her DITHR book. If she misses a word, by guessing incorrectly, point to the word on the page. Typically, you may not even have to say anything, as the pointing may stop her and cause her to reread (especially if you continue pointing to the word until she rereads it). I would also photocopy the Reading Strategies': Student List in the Appendix of DITHR, so she has it by her as she reads. Point out to her that guessing a word is a strategy on the list but that she should use many of the other strategies first before guessing. The list really helps kiddos see that there is more than one strategy to use when you come to a word you do not know!
As far as the vocabulary sheets go, I would use the sheets in the Appendix of DITHR in a round-robin fashion the way that funkmomma suggested. This will give your child a variety of strategies to practice with vocabulary (as each sheet works on a different strategy).

The great part is that your little honey will be learning these strategies and improving her vocabulary right through the books she is already reading for DITHR, which makes vocabulary exercises so much more meaningful.
Happy reading! We are just finishing our last genre for the year of DITHR, which for us happens to be historical fiction. My 7th grader is reading Winter Holiday (from our brand-new Boy 7/8 pack) and my 3rd grader is reading Pioneer Cat (with Hannah soon to come) from the DITHR 2 Pack. Both are enjoying their books. We pray you will enjoy DITHR as much as we do!
Blessings,
Carrie