Here is now I edit out the tripod.  There are so many other ways to do this.  I have found that this method yields the best results 99.99% of the time.  There are circumstances where this will not work.  You will then need to use some other technique.  No one single technique works all the time for every one.  This example uses only Photoshop and PTGui in order to obtain the final panorama.  No other software packages were used in creating this panorama.  
   
The objective here is to give PTGui images that match as closely as possible prior to stitching.  You will not need to assign extra control points or use the Perspective correction feature.  This method may work for other stitchers.  
   
I use a Nikon D300 and a Nikon 10.5 lens.  I shoot 6 around + Zenith + Nadir + Nadir patch.  That makes 9 images total.   
   
Bring your Nadir shot into Photoshop.  CS3 is used in this example.
   
Add an Alpha Channel mask to tell PTGui you want to ignore the tripod head.

Save this as Nadir.tif.  We will use this image during the rest of this tutorial.

 

 

   
   
We will now start building the patch shot.  Start by deleting the Alpha Channel mask you just created.  I know, this seems counter productive, but we will not need this mask for the patch shot.  
   
   
Bring your patch shot into Photoshop.  Select the area you want to use as a patch.  Do not select the entire photograph.  That will only create more work later on.

Hit CTRL+C to copy this area to the clipboard.

Switch over to Nadir.tif.

   
   
   
Remember this spot in the instructions.  You will need to return back to here in a loop and repeat the following steps until the patch is completely aligned.  It usually takes two or three times.  
   
   
Hit CTRL+V to paste.

 

This looks ok right now, but it is not quite there.  Notice you now have two layers.  One is called "Background" (your original Nadir.tif) and the other is called "Layer 1".

   
   
   
Push and hold the shift key while you select both layers.
   
   
 
From the menu, select Edit, Auto Align Layers.

 

Make sure to select Auto.  Press OK.

 

   
 
   
   
   
Photoshop will align the pictures as best it can.

Notice the grey and white squares on the left of the image?  Photoshop had to adjust the background layer.  Notice also the background layer has been renamed.  You now have a patch shot that is getting close to the final objective.

   
   
   
Select Layer 1 only.  Outline the area of the patch to be copied again.  Do not include any of the grey and white squares.  You may see the squares on the right hand side of the image.  Do not include them in your area selection.

Hit CTRL+C to copy this area to the clipboard.  Now you need to undo everything in order to get back to the original Nadir.tif image.  I usually hit CTRL+ALT+Z until I am back to the original Nadir.tif image.

   
   
   
Now go back to the place you were supposed to remember and repeat the alignment steps until you do not have any of the grey and white squares after you do an Auto Align on both layers.
   
   
   
Here is what it looks like when you have finished aligning the patch shot.  You have the original Nadir.tif image with the patch shot aligned as well as Photoshop is going to be able to do.
   
   
Delete Layer 0 by dragging it onto the little garbage can icon in the lower right hand corner.  You now have only the patch shot.  Add an Alpha Channel mask to remove everything except the part of the picture you want to use.

Remember to save this as NadirPatch.tif

   
   
Open PTGui and bring in all 9 images. 
   
   
Select Align images.  You will get control points for as many images as PTGui can create.  I want to give PTGui as little work as possible during the final stitching.  I go to the Control Points tab and delete all control points from image 8 that are not linked with image 7.  I want control points on the patch shot to be linked only to the Nadir shot.
   
   
I then go to the Lens Settings tab and place a check mark in all the boxes under "Shift" and "Shear".  I want to allow PTGui to move the images around as it needs to.
 
I then hit F5 to optomize.
 
 
I then tell PTGui to delete the worst control points.
 
 
After optimizing again, here are the results.

Not stellar, but good enough.  I could play the game of finding the worst control points, deleting them, and optimizing until the Maximum control point distance is less than 2.  Remember, there are 9 images and no control points have been manually assigned at this point.  Everything has been under PTGui's control.  If needed I add vertical control points in order to level out the panorama.

 

 
 
Here is what the final Nadir shot looks like.

There is no way I could get the gradual shading/blending done myself in Photoshop.   I would rather let PTGui do what it does best.

 

 
   
   
I have found that if you give PTGui good images to start with, you will get beautiful results quicker and easier than if you let PTGui to do all the work.  
   
If you have multiple Nadir patch shots (when dealing with tripod leg shadows and such), get then aligned as shown above and bring them all into PTGui.  I have had up to 4 patch shots in addition to the other 8 panorama shots.  PTGui is great at adjusting the images and blending the final output.  
   
Once you do this a couple of times, you will find that it takes only minutes to run through the steps.  I no longer patch the Nadir shot prior to or after stitching.  I prepare the patch shot and let PTGui do the rest.