If the *only* thing you're ever going to use with the splice is a coupler, then the order of the wire pairs doesn't matter. All you need to do is make sure the two ends are in the same order when inserted into the RJ45 jack. The coupler will map wire 1 to 1, wire 2 to 2, etc. So putting the wires into both the RJ45s in the same order will be good enough. (For a flat cable, this means one RJ45 jack will be oriented 180 degrees from the other.)
If there's the possibility you might add networking gear (like a switch) at this splice in the future, then you have to do what bjornl says and figure out whether it's wired as A or B and crimp the RJ45 jacks the same way. I suspect this will require you to cross some wires though, which may not be easy with a flat cable.
If you're going to do this as coupler-only, I actually do not recommend sealing the coupler in tape or something to discourage people in the future from taking it apart. I did that once, then had a problem where one RJ45 jack was not seated fully into the coupler, and had to spend 10 minutes picking apart my beautiful tight tape job in a 115 degree F attic. Just attach a label stating not to remove the coupler, and maybe some string and tape to keep the cable ends nearby the coupler if one of them should come out.