Seems you've gotten confused. The "Windows/Ubuntu:" line is to simply to identify the Operating System the instructions are for, it just means that if you have a Windows or Ubuntu OS then follow the steps below that. You need to copy the "relationships.rpyc" file into the "../game" sub-folder where you extracted the game archive. So, if you extracted the archive to a folder named "Lockdown" then you need to put the "relationships.rpyc" into the "Lockdown/game" folder. You
MUST also delete the "relationships.rpy" (note the missing "c" at the end) file otherwise it will conflict with the "relationships.rpyc" and incest will not work.
From what you say above it would seem that you've copied the "relationships.rpyc" to the correct location but you haven't deleted the "relationships.rpy" file and that's why incest isn't working. If you're not sure which one to delete you can just delete both "relationships.rpy" and "relationships.rpyc" from the "../game" folder and then copy the "relationships.rpyc" from the incest patch archive into the "../game" folder.
Hopefully I haven't ended up confusing you even more!