A quick note on how I manage multiple chart windows. NinjaTrader does not group charts in a single "master" window - which is a bonus when using multiple monitors.

At the same time, it is useful to group some charts together (in a "sub" window), so that you can move those charts together or toggle between them easily. E.g. one may want to bring all EUR/USD charts (multiple timeframes) under one "umbrella" (or, for example, add 6E charts to that group too).

I came across this little application - http://www.windowtabs.com - which does just that. It allows you to group individual windows (charts) in a "tabbed" format (the way most browsers handle multiple windows these days). That makes chart navigation and management much easier (for me, at least).

Free version allows you to add just 3 charts to a "group". Full version is priced reasonably, IMO. Also, note that you can choose (in settings) which application to exclude from "tabbing" (e.g. it's a good idea to switch it off for a browser, otherwise you get tabs on top of tabs which becomes very cluttered and confusing).