The neuropsychologist will choose which tests to use based on which they feel are most appropriate for your child and the referral question. They really do not expect parents to know anything about these tests walking in, or to be involved in choosing which tests to use. That said, it's awesome that you're taking the time to understand them ahead of time - you'll be in a great position to ask intelligent questions and make sure you're getting the most out of the evaluation!
The assessment will include an IQ test, and they almost always start with this piece. The Wechsler Intelligence Scale for Children (WISC; age 6-16) and Wechsler Adult Intelligence Scale (WAIS; 16+) are most common IQ tests, but there are a number of others as well (Woodcock-Johnson Cognitive, Stanford Binet).
They will also have him take a full academic achievement test (reading, writing, spelling, math, possibly oral language). The most common tests for this are the Wechsler Individual Achievement Test (WIAT-3), Woodcock-Johnson Achievement (WJ-IV-Ach), and Kaufman Test of Educational Achievement (KTEA-3).
Based on the results of these two tests and the concerns you present, they will use other tests to look more deeply into areas where he struggles. For example, the Comprehensive Test of Phonological Processing (CTOPP-2) tests phonological processing and rapid naming, which can be impaired in dyslexia. The Beery-Buktenica Developmental Test of Visual-Motor Integration (Beery VMI) is used when there are concerns about fine motor skills and handwriting. They may do some further testing around memory or language, and/or a more thorough reading assessment.
You are absolutely right that they traditionally have looked at the discrepancy between IQ and achievement to diagnose learning disabilities. In the last few years, psychologists have shifted toward looking at the cognitive processes that underlie learning disabilities when making diagnoses, and neuropsychologists are especially well-educated and trained in this area. They will be looking for processing deficits in the areas that underlie reading achievement (phonological processing, rapid naming, working memory, processing speed, etc.) along with evidence that he struggles with reading itself. Most of these areas are included in the IQ and/or achievement tests, but some may require extra testing.
I know that this is a lot, and that I've just thrown even more acronyms and technical terms at you. Sorry!