How are short anime scheduled to be broadcast in Japan?
Bundling multiple shorts into a 30-minute block is reasonably common, yes. Ultra Super Anime Time is perhaps the best known block of this sort, bundling three ~8-minute shorts into a contiguous 30-minute time slot. It was home to seasons 2 and 3 of Miss Monochrome. A couple seasons ago, both Sekkou Boys and Kagewani Shou were on USAT together, which resulted in this bit of hilarity:



However, it's also fairly common for shorts to just be squeezed in between other shows. Japanese television programs don't tend to be rigidly slotted into exact 30-minute time blocks, so you can just kind of put shorts wherever there happens to be room. To use Tonari no Seki-kun as an example - when it aired on TX back in winter 2014, its slot was on Sundays from 26:35-26:45. It was preceded by Saki Zenkoku-hen from 26:05-26:35, and followed by Ichiyazuke (some sort of infomercial) from 26:45-26:55.

Same deal with Miss Monochrome season 1 - on TX, its slot was Tuesdays 25:35-25:40, preceded by Bijo no Kareshi ga Mitai! Osusume (I don't know what this is) from 25:30-25:35 and followed by Gifuu Doudou (which is unintentionally hilarious, by the way) from 25:40-26:10.