Specify the barcodes (indices) either single (only BC1) or dual (BC1 and BC2) or leave both blank for no barcodes
Multiple barcodes can be submitted as a comma-separated list of values
Add target specific primers to the original sequencing primers to avoid using custom sequencing primers, or else, replace wholly with your target sequence (blank out the SP1 and SP2 entries), but then you have to use custom sequencing primers on the instrument. Contact Illumina for gory details specific to your instrument.
Always run the program more than once, to confirm designs and make sure no inadvertent mistakes have crept in, before placing a primer order
