Update: LaTeXTools now supports aux_directory and output_directory via settings or using comments such as %!TEX output_directory = out_dir. There are a few caveats to this support which are included in the documentation.
LaTeXTools doesn't support -aux-directory or -output-directory (yet). However, if you can stomach having a couple of symbolic links in the same directory as your main tex document, you can use something like roeeebar's suggestion from this issue, which adds a settings block to your sublime-project file (I've modified this for Windows, but I haven't tested it).
"settings": { "builder": "script", "builder_settings": "windows": { "script_commands": [ "latexmk -cd -f -xelatex -synctex=1 -interaction=nonstopmode -auxdir=Aux -outdir=Output $file_name", "mklink Output\\$file_base_name.pdf .", "mklink Output\\$file_base_name.synctex.gz .", "mklink Aux\\$file_base_name.log ." ] } } }
This basically places symbolic links to the appropriate files where LaTeXTools expects to find them, so it should continue to work as expected.
A couple of notes:
latexmk is not installed by default on MiKTeX. It's easily installable using the package manager, but because it's a Perl script, you'll also need a version of Perl, such as Active Perl or Strawberry installed and on your %PATH% to get it working. Unfortunately, the usual builder LaTeXTools uses on MiKTeX (texify) will stop with a fatal error if you try to pass it the -aux-directory or -output-directory flags.
You may need to alter the latexmk command of you are not using xelatex.