If you can post pictures of what you need to replace, I can offer some advice. That particular outer sill piece runs from door post to door post, so you wont necessarily affect door alignment. That said, you can be creative in the way you cut out the old and piece in the new. I found that when I started on mine, I actually needed both the outer and the intermendiate sill pieces as there was more rot at the bottom than I wanted to try and fabricate and patch. It was just easier to orfder the new part and install it whole. Now I know I will have no more rust in that area.
Here is what I started with.

And her you can see wher I selectively cut next to the door post on the outer sill

Its sad to say that I will end up with way more new metal on this car than I originally intended; but once I got started I didnt want all of my previous work to be for naught. So in the end I will have a rust free franken spider, but "rust free"

i'm the same as you. once i "committed" to the car (a word used a lot when referring to fiats) i want to do it right. i look at it one small section at a time. make it right then move on to the next section. when i'm done i will have an awesome Spider and an empty bank account. but man! are they fun to drive! i will capture some good pictures of the sill area to see exactly what i'm looking at and post them. thanks again for the help, fellow yankee!