IPhoto & iTunes libraries on USB flash drive. What happens after erase/install?

Not exactly sure how much background someone like Kappy needs for this question but I'll try to not make it a novel.
My late 2010 MBA (64GB) was way low on storage so I decided to get a 64GB USB drive for it and put my iTunes and iPhoto libraries on it. Moving both libraries went exactly according to the instructions. But then after a while iPhoto started to get very slow. The spinning beach ball was running amok. This prompted me to use DU on the new flash drive which didn't show any problems. After doing that I decided to run DU on my mac HD and found a problem that coudn't be repaired without erasing and re-installing Mavericks 10.9.2..
Now, here is my current situation: I have erased and as I write this am downloading a clean copy of Mavericks from recovery. I had backed up everything to my TC just yesterday.
Here is my question:
After re-installing what do I do about telling iTunes and iPhoto where to find the libraries? Or, should I just use the copy of everything that I had backed up yesterday?
Sorry in advance if this is a stupid question. I checked to see if there was some support file for my issue but couldn't find anything that really fit.
As always, thanks for everyone's input. I always learn something from you guys.
Regards, Richard
P.S.: I realize that the problem with iPhoto might not have been the issue with my mac HD and doing what I've done may not fix it. But I wanted to fix the problem with the HD before I went any further trying to fix iPhoto. I hadn't had issues with iTunes functioning with the flash drive, only iPhoto.

Yes, there's no real solution. Apple makes thin, small computers and devices, but of course that means no big drive to store all the bulky media Apple itself promotes on the iTunes Store. You then have to buy external storage which is almost as big as the device you are using, negating the whole concept of a mobile device. I guess you can try wireless, though I can tell you I see about 30+ wireless devices in my neighborhood and with them trying to share only 3 non-overlapping channels I frequently see network slowdown through interference. Of course you bought that nice light computer so you could take it away form home too, but then you are locked into using what's available on the Internet. I guess part of Apple's answer is cloud storage and redownloading. However, Apple itself says you need to maintain your own independent archive: "You always back up your iTunes library in the event that a purchased item is no longer available on the iTunes Store," (http://support.apple.com/kb/ht2519), and, Downloading (using iOS or computer) past purchases from the App Store, iBookstore, and iTunes Store - http://support.apple.com/kb/ht2519 - enabled with iTunes 10.3 and newer; not all media formats are available in all countries (see: iTunes in the Cloud, iTunes Match, and iTunes Radio availability by country - http://support.apple.com/kb/HT5085 ); apps, books (not audiobooks), music, t.v. shows, and movies (some - not all studios have permitted this). Discontinued items not available. For items not included in the iCloud list (e.g., ringtones, audiobooks), or locations or computer systems where iCloud is not (yet?) available, you only get one download per fee paid.
Cloud storage is a convenience but not a replacement for a hard drive at home (and of course, works best when you buy everything from the iTunes Store).

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