".." is not a command. It is an indicator to Linux to look one level up in the directory structure. So, "../tools/configure" tells Linux, "go up one directory, then from there, enter the tools directory and run the command 'configure."
It would be helpful if you could tell us the EXACT error message you receive, and the steps that you are taking that lead up to that error. Most likely, though, your problem is that you are not running the command from the correct directory. You should be running that command from within your build directory, and your build directory should be in the same directory as the "tools" directory.