Mark,
I assume that what you want is your 2D gauges to be visible whenever you start FSX. I'm no panel expert, but I know a little to hopefully be helpful and not dangerous.

The panel.cfg file is definitely the way to go. I'll use a 2D popup panel window in the MilViz C310 as examples.
At the top of your panel.cfg file you have a list of 2D Windows that are present. Each window has separate gauges and are labelled to reflect that:
[Window Titles]
Window00=Main Panel
Window01=GPS
Window02=Throttle
Window03=Copilot
Window04=Engine Panel
Window05=Electrical Panel
Window06=C310 Prelight
Let's use Window01 above to focus in on specifics.
In my MilViz C310, my Window01 section looks like this:
[Window01]
Background_color=0,0,0
size_mm=1280,650
window_size_ratio=1.000
position=2
visible=0
ident=GPS_PANEL
window_size= 0.710, 0.552
window_pos= 0.290, 0.480
gauge00=MPI_GNS!GNS430, 640,0,640,268, 2:1:225
gauge01=C310_XMLGauges!KR 87 ADF, 640,268,640,134
gauge02=MPI_GNS!GNS530, 0,0,640,468, 1:1:225
gauge03=C310_XMLGauges!FBS_KAP140, 640,402,640,163
gauge04=C310_XMLGauges!FBS_GTX330, 0,468,640,170
For the sake of this discussion, we'll ignore the gauges at the bottom, as the principles I am about to share apply no matter what gauges are present. We'll focus on the 8 lines under [Window01], as those are the lines you'll need to tinker with.
The simplest change you can make is "visible=1". Changing the zero to 1 will automatically make the pop-up window visible when the aircraft is loaded (otherwise you'd have to press Shift+2 for the window to appear).
The 'position' parameter lets you place the gauge in a general location on your screen. Your choices are 1-9 (I think). The number 1 is top left, 2 top center, 3 top right, and so on (so, left to right, top to bottom, 3 rows each with 3 positions total). The number 9 is lower right. The 'winow_pos' parameter allows you to finely adjust the window position further.
Regarding window size: You can adjust that using the 'size_mm' parameter, where I think the first number is the window's horizontal measurement, and the second number is the window's vertical measurement. However, I find that adjusting the 'window_size_ratio' parameter is much easier. So, the number 1 is full size, 0.5 is reducing the window size to 50% of full size, and so on. I think this is easier because it preserves the dimensional aspect ratio of the window (i.e. the respective horizontal and vertical proportions are preserved).
There are other parameters, but I never mess with them.
Just remember to save a copy of your original panel.cfg file (goes without saying, I know). Hope this is what you are looking for.
Todd