I have downloaded audiobooks. Manually synced my iphone, and they appear to be on the device when viewing on itunes. But the ipod App on the phone is empty..

Question

Hi, I am going crazy with frustration.  THis is the first time I have tried to download podcasts to my (partner's) iphone.
I have downloaded the latest itunes software. 
Having gone round and round in circles I'm fairly confused over what happened when.  But I got scared when I tried to Apply settings and kept being told that this would Erase and Sync.  ERASE?   Was also told that I wasn't connecting to the correct library, which baffled me.  How did I end up with 2 libraries?  Isn't Apple supposed to simplify this stuff?  Was told that clicking Apply would mean files not downloaded to the Mac would be deleted.  ***?  
I got scared by all these messages and so paid £20 for an app that allows me to transfer files from the iphone to the Mac, because I seemed to be in danger of losing precious photographs.   I actuallly own an Android phone, and all I have to do is connect it to my windows laptop and it behaves like any other storage device, allowing me to copy files back and forth.   But this is not possible with the iphone.  It's a closed device.  Hence the need for software to allow this simple procedure.
Anyway, enough griping.  Sorry I can't be more specific as to how I arrived at this problem.  But the problem IS:
I chose to manually sync files between Mac and iphone.  Selected all the audiobook chapters I wanted to sync.  Pressed sync.  Sync occurred.  According to itunes, the audiobook files are sitting on the iphone.   According to the iphone (looking via ipod App), THE CUPBOARD IS BARE.   No files have been synced from itunes to iphone.  
I have found a lot of people have this problem, on other forums.  But there are no definitive answers.  Just confusion and frustration.   I would be SO grateful if someone could give me idiot-proof advice on how to deal with this.  My partner is counting on me to sort this out, as he desperately needs audiobooks on his iphone so he can decompress from work stress and do some exercise!   As the barely technical-literate one, it's down to me to fix this!
Here's hoping.   If none of this makes any sense, please do ask for more detail, and I will happily respond.
Lisa

Answer 1

You got the new iphone?????   I have same problem.  I transferred audiobooks to device to find no audiobooks on device (despite it being in iTunes as if it was).  Have you found a solution?????   I even tried to change import settings on format transfer but hasn't worked.