You managed to get the patch process started without specifying a patched image? How'd you do that? There's supposed to be pop-up warning if nothing is set when you click the button, and it always shows up when I try it. I'm not always the best at anticipating the myriad ways users will try to break things, though. The readme would have probably helped you, if this is all the problem was.
The patch has to resize files and edit their contents on the fly in some cases. Using a straight PPF for that would result in an extremely large patch file (especially if I ever have to do anything that actually pushes up the size of the patched image). I also didn't want to force people to lose the Kindness Glitch or the Matilda Glitch if they see those things as exploitable fun, so a single PPF wasn't the way to go. You can't patch the same file simply because the tool has to have a pristine copy to start from, and in the event something goes wrong, I don't want people to have to reacquire or recreate the original.
The file size post-patching will be the same. The game has something like 200 empty sectors at the tail end of it for padding, and the patcher will write as many sectors as it to takes to pad the image to the size of the original. In the case of the NA game, I think it needs to write something like 10 fewer to pad it, provided you selected the Trade Rumors patch.
The easy way to tell is to compare checksums (MD5, SHA1) for the source and target images, but I can't provide a reference sum for the patched image, as your checksum will vary depending on what patches you selected. It might be worth adding a small bit of text on the title screen, bottom left or something, just to let people know it's a patched image, but it's not something that's done now. I always thought it a little too intrusive. The earliest opportunity to confirm would be to try the Inn Bug in Ryube, provided you patched it.
Edit: That being said, if the patcher succeeds, and the patched image file exists and can be read, it's a pretty safe bet things worked. There's also a log you can look at in the patch directory to see what it did. There are a lot of steps to comb through, though.