Popping an RJ45 at both ends is not a the correct way of testing any network cable, A continuity test will only establish path between two points and confirms if it can communicate. However to answer your question, this will work but will not tell you if you are picking up any interference, high frequencies, which in turn slows down the performance of your network cable etc etc.
I dont want to scare you off, I'm just stating the correct way of testing and installing the cables. As DoogyRev suggested, test first with loads of RJ45 and spare cable,
You want to wire the network cable as a straight through. This also applies to patch panel and wall sockets see diagram below. This diagram is using the T568B standard, which is pretty much the norm and universal standard.
I hope this helps
What tester did you purchase?
P.S.
When crimping or creating a network cable untwist the pairs, and arrange the wires in the order of the desired cable end, Trim the ends of the wires so they are even with one another, leaving only 1/2" in wire length. If it is longer than 1/2" it will be out-of spec and susceptible to crosstalk,which again can reduce performance of your network cable.