Assigning the build will just help with organizing the data for most tools, but some do interpret this metadata and use it (many Picard tools work this way). Plus, assigning at upload is less tedious than clicking into the individual dataset pencil icons and assigning after.
Be sure to assign the correct type. Simply using "fastq" is ok if you do not know if the data is "fastqsanger" yet (what most tools require). If all data are similar, upload one, test to see if "fastqsanger" can be directly applied, or if running the FastqGroomer is required. Here is how to check: https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA
Good question, will help others to use Galaxy efficiently and avoid input format problems (it really is the most common reason for tool errors based on my experience). Jen, Galaxy team