Controlling The Data Flow And File Sharing Between Computers Is Slow?

I have 2 computers in my room which between them i very frequently share files between. Wirelessly they were both connected to my home's router until recently the router was removed, but will be back soon.The problem though, was that with using the router, file sharing between those computers was slow, and with the router gone, I was lost because there was no movement of data between the computers whatsoever, I had no crossover cable, but plenty of regular ethernet cable. Than I remembered something about gigabit lan not needing crossovers(both of the computers being gigabit) and I connected them, and marveled at the new way to share files. And more by the exponential boost in speed(800kb/s to a grand 12mb/s{though I still think that is slow for gigabit.}). Obviously I've overcome a problem, but that's not where this story ends, it comes with another problem. When the router is reconnected to these computers, will the files still transfer through there new found direct connection? or will it attempt to go through the router, only allowing me to get the speeds I want when one of these computers isn't connected to the router?