I wanted to say thank you to all the people who give very good suggestions and comments, even the bad comments are good.

I have figured out how to set my camera up using the manual settings and playing around with the white balance settings so I can try and even up my light differances between the two shots.  Can someone tell me what is the best settings to soften the window shoots in my virtual scenes.  When I take a inside pix, I have my settings on  20 / F2.8.  Any suggestions so I can look out the windows instead of seeing a bright glare?

I take between 10 and 5 exposres per hemi. Each exposure is one stop. White balance is set to cloudy. Shutter priority.
1/500
1/250
1/125
1/60

and so on.

I have a complete bracket set

I look at these exposures and pick the one that has the best windows but is the lightest without loosing window detail. This is the base image to start with. Tip-this is usually the 1/250 to 1/60 exposure. Make sure you select the same hemis on both sides or you will get a color imbalance.

Using the PS plugin for layer masking found at http://www.erik-krause.de/index.htm?./blending/ I then create a HDR hemi. Now you can see out the windows.

Do this for each hemi.

Stitch and you have a good looking pano.

Gen. Lee

You mentioned " When I take a inside pix, I have my settings on  20 / F2.8."  

At f2.8 you will have little or no depth of field.  Meaning that your foreground and background will be out of focus and mid point will be the only objects in focus.

Suggest that you maintain f8 or better and let the shutter speed float.  F8 seems to be the 'Sweet Spot' where all fore, mid and background will be in focus.