EQ2 does its own windowing, and its own resizing, so WinEQ doesnt mess with that for EQ2.
There are two things you need to know about with EQ2, if it is indeed set to windowed mode:
1. The UI is based on the size of the window itself. The EQ2 UI assumes a MINIMUM window size of 800x600. It will move elements down and to the right if you stretch the window, but will NOT move elements up and to the left from that position -- so if you make the window smaller, the UI windows for EQ2 will not be moving where you would think they might go. They just sit there. And do nothing. This is briefly noted on the EQ2 features page for WinEQ 2 as follows "Note: Due to a bug in EverQuest II with resolutions smaller than 800x600, some features are currently less useful than normal (Tiling and Picture-in-Picture are affected for example)"
2. The game display is based on the Direct3D resolution, which in EQ2's case, is resized along with the size of the window. However, unlike the UI, the game display is NOT assuming a minimum size of 800x600. This means that although the game itself might be at a tiny resolution of 256x192, the game's UI is still at 800x600, and only the upper left corner of it would be visible.
And if the game itself is set to full screen mode:
1. The game resolution is limited to at least 1024x768 in full screen mode. The UI is based on the size of the window itself. However, instead of leaving everything as if it's 800x600 resolution or greater, a portion of the UI is simply
not drawn. The amount of the UI not drawn is equal to the scale of the current window size to the Direct3D resolution. So if the full screen mode is 1280x1024, and you've sized the window to 1024x1024, 1024/1280 of the UI will be visible height-wise. The visible portion of the UI is also scaled along with the window. So is how the game uses the cursor, so moving the mouse over what appears to be somewhere... doesnt work right.
The problem with windowed mode is scaling smaller, and the problem with full screen mode is scaling at all. By EQ2's design, it's just a pain in the ass

I can change the behavior for its full screen mode to be a little more friendly, but keep in mind that scaling the display instead of the game itself changing the resolution is going to hurt the quality of the display, and possibly make text fuzzy or harder to read, etc.
I can pretty almost guarantee though that I cant reliably fix the problem with windowed mode not scaling the UI correctly below 800x600.
I will look into a solution, but keep the above in mind. Let me know what you think