Import the ALAC files into iTunes, make playlists of tracks you want on the device, check the Convert higher bitrate songs to 128 kbps AAC option. Then use the Sync with selected playlists. Your device will get the downsampled content while you can enjoy it at top quality in iTunes. Any updates you make to your content in iTunes, tag corrections, rating etc. will still be copied to the devicebut you don't have to worry about maintaining the separate sets of media files or updating two sets of metadata.
When you drag & drop files into the iTunes library it just adds them, either linked to where they are or by creating copies depending on your settings. If you're running Windows then you can add WMA files and they will be converted according to your choice of rip settings. Once files are inside your library you can create duplicates in an alternate format/bitrate by changing the rip setting and then using the Convert to <format> tool.
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