Jumper settings are quite clear in the manual. JP1 enables keyboard power-on, but I'll leave it off (default) for now. JP4 is for clearing the CMOS.
Connecting the case switches and LED leads is possibly the most fiddly bit of the whole process. Well, in close competition with fitting the heatsink.
Aside from the connectors being small, the labelling on the board can be different from that of the case. However, at least the cables are different colours, making it easy to trace each wire back to the switch/LED on the case. Some connectors are grouped in pairs of pins, often pin1 is labelled with a small triangle stamped into the plastic.
Connect the case speaker cable to socket SPK1, which is easy if its a block of 4 pins (orientation doesnt matter).