It looks very much like the pilots have to operate in unison while controlling the Jaeger machine, and that some orangey organic fluid fills up their suit in the process.
Also, io9 (via Toronto Sun) that the A.I. behind the bots is voiced by Ellen McLain aka GLaDOS from Portal. Says director Guillermo del Toro:
I wanted very much to have her, because I'm a big Portal fan. But just as a wink. She's not cake-obsessed. She's not out to destroy humanity. I said, ‘Look, there's no A.I. I'd rather have than GlaDOS. The filter we're using [in the film] is slightly less GLaDOS. Slightly. The one in the trailer I wanted to be full-on GlaDOS.