You don't have to buy smartftp as it's trialware.
You can use any ftp client so if you're more familiar with another, you can try using yours instead. (Some just might not have the skip function.)
You can get smartftp at:
http://www.smartftp.com/download/ Unless you're sure you need the 64 bit version (unlikely), get the 32.
You will also need your ftp info: host address (e.g. ftp.yourdomain.com), username and password. It should be the same info you used in ootp.
Once you install smartftp, type in your host address in the address field at the top of smartftp, then your username at login and password in password. Once it connects, navigate to the folder where your files are on your ftp site. Now here's the tricky part. Make sure all those old files are deleted from your ftp. You could either delete those one by one, but I'd just all your files in that folder as that would probably be quicker and surer in the end. Then in another frame use the local browser feature (if you don't have 2 explorer-like frames, click on the icon of a folder with a magnifying glass) to locate your files on your computer. Once you have, select the files you want to copy and drag them over to the folder you want them to be on your ftp site. Once you drag them there and release the mouse button, they should start copying. Now if you deleted all the files in that folder (instead of just deleting the ones that did not update) it should be simply copying them for, as far as it knows, the first time. Once it appears done, do it again. Now this time (or the first time if you just deleted the files that did not update), a dialog box should pop up asking if you want to "overwrite, skip, or abort". It's asking you this because at least some of the files already exist. What you want to do is now skip the existing files because they should already be up-to-date, but before you click on skip, check the all box so you don't have to click skip repeatedly. Once that's done, it should copy the files that did not copy the first time and all your files should now be up-to-date.
So why doesn't it just update them all the first time? I don't know. Sometimes it does for me and at others it doesn't. Somebody else probably has a better idea why not.
If you get stuck on the ftp stuff, go back to that smartftp site and read through some of their support tutorials. Once you get the hang of using an ftp client it's a snap.