Do I need to do anything different when pasting the calendar into a separated system?
Not really. Of our two integration methods, if you're linking the calendar (instead of pasting it into your file), separation isn't an issue at all. The calendars events table (along with contacts and projects) will be in your data file but the other tables can stay in our calendar file.
If you're embedding the calendar into your file, then the graph shown in our integration article should be in your Interface file just as it is shown in that article. All the layouts mentioned there should be in your interface file as well.
The SampleEvents table there can be in another file (your data file, presumably).
Color Coding in Separated Files.
If you want to show an event's color "on" the event record in list view and in the Event Details mini window, follow these instructions.