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.

Questions:
-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