Is it necessary to preprocess whole genome short reads from NCBI before aligning them against a .gb reference? How if yes?
If "pre-process" means scanning for adapters/trimming of adapters/adapter dimers then the answer is yes. If there is no contamination present, the reads should come through unchanged. There are many programs that can do this part. BBduk from BBMap, Trimmomatic, trimgalore etc.
What .gb reference are you going to align to? In general, NGS alingers will require you to create aligner specific indexes from a (multi-)fasta sequence of the genome you are interested in before you can do the alignments.