1) Will the PB play the wave files and navigate through them with just the file structure that I am using? (This is only until I am set up with FLAC)
Yes, the default music application will work fine with this setup.
I have been wanting to convert all of my wave files to FLAC lossless with id3 tags. I bought the HD-1000 because it reportedly will play FLAC files.
Yes, there is a 3rd party codec available to play FLAC (as well as WavPack).
However the first thing you will need to do is upgrade the firmware on your PhotoBridge. The HD1000 comes with 1.5.18 installed, this is quite old and missing a number of features, including the ability to support 3rd party codecs.
You'll need a compact flash card in order to upgrade your firmware.
This posting gives a link to download version 2.0.36 of the firmware (the current latest), you would download the file formatup.rok to your PC, put this file on a compact flash card and place the card in the HD1000. Hold the power button on the unit down for at least 5 seconds (till you see the light flashing) and then wait several minutes while the HD1000 upgrades. After its finished upgrading make sure to remove the formatup.rok file from the compact flash card.
At this stage you should be running 2.0.36 and able to support 3rd party sound codecs.
The FLAC codec can be downloaded via this post
Instructions to install are in here also.
For bulk transcoding/conversion I would use dBpowerAMP
specifically the dMC File Selector tool within dBpoweramp Music Converter application.
This can convert your files and keep the directory structure intact.
For bulk tag renaming I personally use MP3Tag
using the "Convert -> Filename - Tag" option and a format string something like
This has a preview feature so you can test/see what the resultant tags would be.
FLAC files use an ID tagging system called Vorbis Comments (also called FLAC tags). The default music application does not support this tagging system, but you'll still be able to play the music fine (once you have the FLAC codec installed obviously).
However there is an application for the HD1000 that does support FLAC tags, this is called Sonica.
The default music application (called Listen or Sonata) only supports ID3 tags, which is what MP3 files use. However, the lossless codec WavPack can also support ID3 tags (as well as its main tagging format which is called APEv2). I'm just mentioning WavPack as its an excellent lossless codec also, see here for more info if you've never heard of it.
I know this is a lot of information to get through, but hopefully this should get you started.