They go in the server/maps directory. You want to keep /maps and /quests in your server directory, so that they don't get changed when you do upgrades to the emu code.
You can run the ifconfig command from your linux terminal window and it will tell you the IP of your server. That is the IP you will need to set the Bind Address to in your my.cnf file.
Make sure that the changed you made to the file actually saved. That file is set to only be editable by root, and the only way I know of to do that from the Linux PC is either VI, or to use chmod to change the file access properties so that your normal Linux login can save the file and then you have to set the properties back again for mysql to use it. It requires a restart of mysql for these changes to happen, but you can just restart the whole PC to make it simple.
The way I normally edit that file is using the webmin tool. If you haven't set that up yet and checked it out, I highly recommend doing so
You can log into that tool as root and then you can edit the text file and save it directly without having to use VI or having to change file access properties.
As for the RAM, yes it will go up as you get more players on, but normally it will go back down again when there are less players. If you have more than 1GB of RAM, you probably won't ever have any page filing, as it will all stay in RAM, which is better anyway. Occasionally something happens that starts using up my RAM and I have to restart the server to restore it to normal, but normally it can run for quite a while before there are RAM issues. RAM usage will go up the more players you have on, but even with 120ish on my server, I have never seen it go over 1.5GB of RAM usage.
I think that you should be able to work on getting your Windows to Linux Mysql connection working without effecting your players at all. You can just keep the server running the way you have it now until you can get that connection working. Once you do, then a simple database dump and move then source it and change your settings back to your Linux database and you should be good to go
