I don't know how your program works, but I do 
this.  Probably you have similar commands in your 
software.

1.  Create a "new" file that's blank.  I'm asked 
how big I want it and other stuff: I make it as 
big as the program will let me and otherwise 
match the perimeters (type, dpi, etc.) with the 
scanned files I want to merge.

2.  Paste one of the scans onto the blank file.  
I start with the one on the left, but you can 
drag it around if you want to put blank space on 
the top or the left.

3.  Paste the other scan and drag it around until 
it lines up with the first scan.

4.  Crop the new file to include only the cel and 
save it.

That sounds easy, and sometimes it is, but 
sometimes it's tricky because the colors on the 
two scans are just a little different or because 
(sigh!) one of the scans is crooked and will 
never exactly line up with the other now and so 
you gotta scan it all over again...

But usually it works.  I had to put one cel in 
the scanner four times and eventually all the 
parts fit together.