To simply convert files from Windows WAV to FLAC on the commandline the official tool flac would be the obvious choice.

flac ~/Music/*.wav

would convert all WAV files from the Music directory in your HOME to flac. By using the option:

flac --keep-foreign-metadata ~/Music/*.wav

even non-flac metadata will be preserved in your resulting *.flac file. However if - as you say - your files are not tagged there is not an easy way to achieve correct metatags. Some tools like metaflac from the flac package can import metatags from file but these files need to meet specific criteria for appropriate tag recognition involving conversion of your XML file.

Therefore I would rather recommend one of the graphical solutions like Ex Falso or Musicbrainz Picard that offer the creation of metatags from filenames (in case they are appropriate).

Picard also has a tool to auto-recognize a not tagged song to look it up in the Musicbrainz library and create appropriate metatags.

Before playing around with tags it is strongly recommended to backup your original files in case something goes wrong. I speak of own experience when tagging of multiple files resulted in entirely wrong and bad tags that led to almost unretrievable originals as these files were listed with a (random) wrong name in my library.

Use Rhythmbox

Ubuntu's default music player Rhythmbox can Sync music with iPhone and other iDevices:

or there is another program:

gtkPod

This can be installed from Ubuntu Software Center.