One of Pixie's cool features is that it can provide you with information while you are playing EQ. It does this primarily with its Alert window, but also by allowing you to put Pixie's windows in front of EQ if you choose. Below is detailed information about Pixie's windows staying on top of EQ. Most people only need to know the more practical information provided in the Overview.
EverQuest must technically be in "Windowed" mode for you to see Pixie's windows while playing. However, Pixie will make EverQuest appear to be in "Full Screen" mode. In fact, most people think EQ is in Full Screen mode while Pixie is running.
What does this mean to you?
You should keep EverQuest in it's internal Windowed mode. If you switch EQ to Full Screen, by pressing Alt+Enter or via EQ's options, then you will no longer be able to see Pixie's Alerts. (You can disable alerts in Pixie's Options if you wish.)
Switch to Windows by using Pixie's customizable hotkeys instead of Alt+Enter.
EQ1 will look best when it is set to the same resolution as Windows. Because EQ1 is in Windowed mode it is being displayed at the same resolution as Windows. You can run EQ1 at other resolutions, but it will be scaled to fit the Windows resolution. EQ2 automatically adjusts its resolution so you don't need to worry about this.