Presumably you didn't run "xconfmanager -fp" after doing the edit...
As for having separate log files for each process, that's actually pretty important to avoid bottlenecks around syncrhronizing writes to log files across processes, to avoid having to add information to each log line/event to distinguish which method server it's coming from, and to make the sequence of events within each method server easier to follow.
As for searching across log files, see wtcore/jsp/jmx/logFiles.jsp (or use grep if you're command-line-inclined -- in which case you should be using Linux/UNIX or have Cygwin installed). Also, see wtcore/jsp/jmx/logEvents.jsp for a unified view of sufficiently important (warning and error) log events. [Of course both JSPs require 10.0 or higher.]