There are two ways to convert:
1. Library Tools > Convert Format
2. Handheld Sync
Convert Format is a manual conversion tool. Use it when you want to force conversion of files. It includes options to include the converted files into the library.
Handheld Sync uses one or more playlists/smartlists to control which files are transferred, and the transfer is based on the settings configured in the HH profile. This profile can include conversion, and the transfer to can to either a HH device or a folder. It retains a list of already transferred files so future syncs are more efficient.
Which one you use depends on your needs, but the best way to learn is to experiment with what works.
Both of these mechanism will use a conversion cache it MC is configured to use it (it is by default). The cache location / settings are defined in Tools > Options > File Locations > Conversion Cache. I disable it, as I already create a set converted files via HH sync.
Each encoder has different profiles. The four modes you ask about re. the MP3 encoder are four typical levels of quality vs. space, the standard trade-off with lossy encoding.
The duplicate files you see are probably because you used Convert Format and included the results in the Library. You don't have to include these, but if you want to, you can just configure your views to exclude them, or separate them in the view for easy selection. It really all depends on what you do routinely. Again, experience will prove to be the best teacher.
As for your speakers, check the settings under Player > Playback Options.
Thanks for your comments MrC! The 4 modes I was talking about are listed under mode in HH Sync: Original, Specified output format, Specified output format only when necessary and Specified output format only when necessary (inc.high bit rates). The 3rd one is checked by default. I'm not sure which one to choose.
In terms of duplicate files, I was using HH Sync and unlike using Convert Format, there is no option to choose not to include the converted files in the MC library under HH Sync options. At least that I can see. I only want those converted files on my phone. I don't want them on my computer taking up space and I don't want any duplicate files that I need to remove or whatever. I've disabled conversion cache as you suggested.
Info from JRiver: There are two different ways you can sync.
1. Drag and drop -- Just open "Sync to Handheld" or "Sync to Portable" in the Action Window (lower left). Then select the files you want, and drag them to the Action Window. Repeat until you've got everything queued, then press the Sync button.
2. Playlist Sync -- Use MC's options for Handhelds (aka Portables) to set your choices. You can select your own playlists, or you can select categories like "All Audio". Once you have it set, choose Sync in the Action Window.
I used the drag and drop under HH Sync. I do not have any playlists or smartlists set up. I could choose "All Audio" which is what I want to do - have everything in my library converted to mp3 and deposited on my phone. But I don't want to go ahead and do that if every file will end up being duplicated in MC.
And I was able to solve the speaker issue by enabling my Audioengine D1 in the options menu in MC19 - somehow it was not enabled.
Thanks!