The basic idea
The characteristic "wobble" bass popular in mid-late 2000s dubstep is frequently (but not always) created by sweeping a lowpass filter over a harmonically-rich sound of some kind, usually some oscillators. The filter cuts out the higher harmonics, creating an effect similar to closing your lips while saying "ahhhhh. By moving the filter cutoff up and down rhythmically, you create the basic wobble.
There are a million variations on this as well, such as using distortions, different filter types and settings, simultaneously bending the oscillators' pitch, and using frequency modulation (FM) synthesis to change the harmonics around instead of a filter. If this is an area of sound design you're interested in, it's worth experimenting as there are a lot of interesting sounds to discover.
Audacity does not, as far as I know, support modulating an effect's parameters over time, so there is no way to move a lowpass filter rhythmically.
A very common approach to doing this in software is to use a software synthesizer, usually a plugin in a larger DAW program. The immediate advantages to this are that you have a very straightforward way to play musical notes on it (most of them support MIDI), automate your filter (either via the DAW's automation features or a synth's low-frequency oscillator), and record what comes out.
DAWs and synths are not the only solution however. As ObscureRobot pointed out, you could use a programming environment like Pure Data or Csound, or anything else you can come up with. Your idea of using a pair of low-frequency sinewaves and relying on their beat frequency seemed very clever, for example, and there's surely something you can do with that too.