Look in the .conf file for the Modules section and set the modules dir to the dir the modules/ dir is. e.g. Mine is modules/ .. yours should be modules1.6.1*/ if you haven't used the 'make install' and the * is the last digit of his version. Or like this should be. A friend of mine had a problem like this to, and fixed it after changed the modules dir in the conf file as it corespondes in reality.
Once the game is over, the king and the pawn go back in the same box.
When eggdrop is compiled, it generates several files. The main executable, and a relevant number of *.so modules, depending on what you picked at configure time.
These files are located in the directory where you typed "make".
However, by default, the config file is setup, to be used of a fully installed bot. This means that the *.so files are contained in a modules directory (named after the eggdrop version, but symlinked to "modules").
Simply compiling and running is suficient to get the bot running, though you will have to tweak the config file.
To save doign this, follow all of the compile instructions, inlcuing the "make install" fase.