This is how I use it:
File>New>Audio Montage>set samling rate. Multitrack window opens.
Right click on the track number ("1") on the left of the multitrack window and select "add stereo track" which should be at the top of the list. You now have two empty stereo tracks.
To add files, right click into the tracks and select "paste audio file(s)". When both files are open, look for transients that stand out in both files and use them as reference points to set the delay between the two files, i.e. move the sbd file "forward" until it syncs with the aud file. This can be difficult and I'm not sure if there a "right" way to do it. Use your ears.
You can add effects to the individual tracks in the left part of the multitrack window (where it says "no fx") or to the master bus.
If you need to resample and add dither, you can do so during the mixdown by adding the "crystal resampler" plugin to the master bus and turning on "dithering" as you would normally do when working on normal stereo files. Hit render and get a cup of coffee.