I have multiple HPUX boxes all with the same kernel settings, is there a HP-UX equivalent of /etc/system that i can scp over to the other servers so I can automate this?
/stand/system is the file you're looking for in HPUX.
so just copy that file over and reboot?
Sorry. I can't answer that part 
The procedure to build a kernel varies quite a bit from one release of HP-UX to another. Here is a link to one of the procedures. I do not recommend copying /stand/system from one system to the next. Note that the procedure documented in that link does not trust /stand/system even on the box it was created on. The HP procedure recreates the system file each time a kernel is built. Also, depending on what you want to change, you may not need to rebuild the kernel. Again, stuff that is dynamicly reconfigurable also changes from release to release. You really need to look up the procedures for your HP-UX release and follow those. If the boxes are absolutely identical, copying /stand/vmunix over might work. But that is dangerous and could result in an unbootable system if anything goes wrong.
its 11i and i guess /stand/system editing directley has been deperecated...
but there has to be away to send these changes out to multiple identical boxes
The easiest way if you're not familiar is to use SAM to build your kernel.
(For some reason, HP have removed it from 11i v3 - still, they're making all sorts of strange decisions these days.)
My understanding is that they replaced SAM with a new package but I have never used 11i V3.
you need to copy both vmunix and system. But the OS version and the hardware version are has to be same.