If you upload a page with the same name as one that is already there it will indeed replace it (but CuteFTP will ask whether you want to overwrite the existing file so you will know that you are doing it).
Did you keep a copy of the original pages? If not just download them again but save them to a different folder, then you will always have a copy if you want to revert back to the original.
What is probably happening is that the font size is being specified inline for those particular words and it is overruling the font size that you are putting in for the whole paragraph.
If you click the HTML tab at the bottom of the screen you can edit the code to get rid of the tags that are making the font a different size. Find the word(s) that is the wrong size. If it is text that you pasted from the PlusNet wizard page the word(s) will be surrounded by something like this: <font color="#0000FF" size="6" face="Times New Roman">your text...</font>. If the text is some that you have written in Nvu you will be looking for either <big>your text</big> or <small>your text</small> tags around the text.
Which ever is the case if you want the text to be the same size as the rest of the paragraph just delete the pairs of tags.
Keep going - you'll get the hang of it soon. If you think that it might help I'll gladly create a page to get you started. On the other hand I'm equally happy to carry on helping (as best I can!) on here.