Yes it is perfectly fine to mess with the configuration of each ini. In fact, to get the most out of MQ, you probably should change settings in the ini files.
First the bot_toon_class.ini. As stated earlier, this is for the bot macro. If you plan on using the macro to play your character, you must edit this ini or your character will just stand there with a thumb up its butt. The macro has the benefit of being totally customizable and, if something is possible to do with MQ, you can usually get the bot to do it and play the character how you want. Also, if something changes in EQ, you can generally edit the bot macro yourself and fix any bugs. The downside with the macro is it takes a lot of time to get it set up properly and you have to know your way around TLOs to get it to function the way you want. Also, Pete has stopped supporting the bot macro and began focusing his attention to the plugin. Thus, any new features will likely not come to the bot macro.
The server ini that you mentioned is for multiple plugins. Settings for things like MQ2Melee, MQ2Bot, among other plugins will be listed here. Before you go through and change settings, I would advise you to read the Wiki for the plugin you are changing to be sure of what you are doing. Most plugins work fine out of the box but you can get a little more from your characters by adjusting settings here and there. MQ2Bot for example will work to about 80% of your characters capacity with no changes. Making some adjustments here and there will get it closer to doing what you want.
