jal pay
They get extra pay if they fly long haul. So now 777 is the one flying to Europe and East coast.
737 and 767 are mostly flying for Japan domestic, China and South East Asia.
They get little extra pay from those flight if they fly red eye.
777 is the only same fleet btw JAL and JAS. Those pilot group are flying together with one OM now. Other fleet like A300 and MD90 are still flown by JAS guys.
According to the pay scale, JAS guys used to make more than JAL, but now JAS guys make same as JAL guys make.
And about the base, as someone above said, no bidding system in Japanese Airlines.
JAS has Tokyo, Fukuoka, and Osaka base, and JAL only has Tokyo base now.
Normally company orders where your base is, and supports complete relocation.
Hope this help.