I think the first request has to do with making msg windows desktop windows. If that is the case, it would be in the same place in the options as the setting for channels (alt+o -> +display -> options -> Windows... button), but they are called "query" windows.
As for the 2nd request, it is true that control codes are stripped from .ini files. If you want to keep colors in there, make a simple on start script like this:
on *:start: timestamp -f ( $+ $chr(3) $+ ##HH:nn $+ $chr(3) $+ )
where ## is the color number (2 digit format, like 04 for color 4, prevents the numbers in the time from being treated as part of the color code). $chr(3) returns the control char for color (ctrl+k). Other useful codes are $chr(2) for bold, $chr(22) for reverse, and $chr(31) for underline.
