The GSA Indexer software is somewhat strange to figure out in terms of its queue. You can add url's or multiple url's to it and it'll sequentally run through them, but while it's running you can't add or modify anything to its current queue. You have to actually stop the queue in order to add your own URL's, and there's no indication as to whether or not it will continue from where it left off after clicking start again or if that queue is lost forever.
It would be nice if you could manage/modify its queue separately from its running process.
Or I'm totally lost and just don't get it ... ?