If your cooler came without paste pre-applied then definitely add your own!
Some mobos come with a little plastic block for the front panel connectors (power, reset etc) - you plug the wires into the block and then plug the block into the mobo. Makes the task much less fiddly as you can connect the wires up outside the case and then just plug one thing in!
I do:
Mobo
Cpu
Cpu cooler
Psu
Ram
Gpu
Fans
Hdds
Then cable manage the lot, triple check everything, first boot, install os, remove windows crap, drivers etc etc.
As for connecting up your front panels to your mobo, it should have clear markings what goes where, front panel usb, audio and usb 3 If your case has it will only fit in the correct plugs.
To connect up your power and reset buttons etc again that will be marked( although the writing is usually small) on the mobo, normally at the bottom right.
guys im completely stuck on the cpu cooler, it shows on plenty of vids that you need to attach a back plate on the underside of the mobo, but on the x99 mobo there are no holes to insert the back plate... does any one know if I should skip this step or make drill holes on the mobo?
all the vids show its on lga 775 1366 1156 ect, but no tutorial vids on the x99
the instructions have nothing about the x99 chipset, all I have is a packet with 4 mounting screws.... I think the x99 is new hence the instructions are not there...
I cant see anything on google either
who else has built a cpu cooler on a x99 chipset? can you remember?
Please do not drill holes in your Motherboard. From the looks of most x99 boards you don't need the backplate, check this video for AIO install.
It's for the H100i but the same priniple will apply to other AIO's.
The cpu and opt cpu are both just for your cpu fans incase your using 2, i wouldnt have thought it would make a difference which you put it in, just stick it in the first one.