Devices, desktop player, formats, etc

I collected mp3s for years with Winamp, then went to itunes. It F'd up my library--tried to do it all automatically. I got it humming along finally. Went to Itunes match and it F'd up my library. Songs stopped short, songs were removed from the albums. I re-scanned my CDs into AAC compressed files being led to believe that they were better than mp3...then I rescanned things to Apple lossless because I could go to any format from there...

I think I need some experienced coaching here.

I have an ipod classic 80GB and an iphone 4s.

Now I discovered 24bit audio downloads (usually FLAC), Audioengine D1 USB DAC and Audioengine 5+ speakers will transform PC audio. So now I have a bunch of 24 FLAC files which play well on the desktop, but won't play on an ipod without conversion.

I downloaded J River MC17 to evaluate. I like the extensibility but the learning curve has been a bit high. I know and understand Winamp, but its UI is a bit limited after seeing Media Monkey and MC17.

I have 10K songs.

-It looks like itunes is almost required for iphone synch, so is it best to let it do ipod and iphone both?
-Now that I have a bunch of FLAC files and itunes won't downcompress them for ipod...what should i do? Go to all Apple Lossless?
-or should I convert all my Apple Lossless songs to FLAC, then use DBPoweramp to build an mp3 library? Sounds like too much.

I'd like to have one player/library manager that can handle all the file formats transparantly and down convert them for ipod/iphone synching. Is this over the top and too much to ask?

I am confused and tired of scanning my CDs over and over into new formats. I know that I can convert to lossy formats after they're in a lossless one. So the question remains (which lossless format buys the most flexibility in your opinion?

Your opinions are welcome and will be appreciated.

BannonB, I batch converted about 250GB of ALAC files into 50GB of 128kbit VBR AAC and put it on 64GB microSD card. I use it in my Samsung Galaxy S3 phone. MAX is for Mac but there are similar programs for Windows.
I have started ripping music with MC17 to FLAC, because it doesn't like some of the naming conventions iTunes adds to Apple Lossless rips; MC17 names and files some artists differently, for example PJ Harvey. I had to re-rip all of her stuff because JRiver mis-named and mis-filed the apple lossless iTunes rips.
Have researched this issue, maybe the answer is DB powerAmp, maybe apple lossless rips from that will import correctly into iTunes and JRiver, who knows. Otherwise you have to use after-market software (free) to convert the FLACs into Apple Lossless files, then import them.
If you are simply managing iPhones and iPods and iPads, iTunes is fine. Once you get into PC audio, you need to use JRiver on a PC or use a plug in on a mac with iTunes.
I don't know anything about playing 24-bit, high-resolution music in iTunes or on phones/ipods/ipads, so I cannot comment on that...
BannonB, one sentence appears to be missing in my post. MAX is a free utility program for Mac that allows to rip CDs (better than I tunes) and batch-convert any format to any format.

Ideal program should rip CD as data (I set MAX in that mode) forcing to read the same sector over and over again until right checksum is obtained. Itunes reads CD as music meaning that scratches up to 4mm along the track will be error corrected, 4-8mm will be interpolated and >8mm will result in gaps.