Do I need to resequence one long region or may I also use this to sequence several shorter ones?
It's possible to tile either a single contiguous region or multiple dispersed fragments. From an assay perspective, a lower number of PCR amplicons required to resequence the desired regions will simplify the pooling procedure. Affymetrix provides a validated long-range PCR protocol to help users reduce the number of amplicons needed. See the GeneChip® CustomSeq Resequencing Array Protocol for details.