Step 1 (Sub)
Find a kick drum sample that you like, and tune it to the key of the track that you are working in. I've previously written on how to do this, in short this means just placing your kick drum at exactly an octave above your bassline so that they don't occupy the same frequency spectrum. Protip: If you are starting out by writing the drums what I like to do is to tune my drums in the key of F and go back and readjust this if I move to another key. This is because F is usually the lowest note that can be replicated well which is especially important for a bassline. A large amount of Drum and Bass and other forms of electronic music are written in this key as a result.
Once you've tuned the kick drum so that it's peaking at the correct frequency, grab an EQ and drop it on the kick's channel as an insert. If for argument's sake you are writing in F then your kick drum should be peaking at 87 Hz or so. Put a high pass filter (HPF) on the the kick drum with the EQ you've just added, and set the turnover frequency to exactly an octave below the kick drum's peak. In the example we've been using where the kick drum is peaking at 87 Hz, this would mean placing the HPF's turnover frequency at around 43.5 Hz which will just cut out any uneccessary rumble. Beware, a large number of kick drum samples will not sound good when pitched up to the 87 Hz range, so you will need to be selective. Adding some distortion or a bitcrusher can bring some of these frequencies back, just make sure you do so in a CONTROLLED manner after the EQ and compression stage.
Next, do the same thing but with a low pass filter (LPF) however this time set the turnover frequency an octave above where the kick drum is peaking. Going back to our example once again, where our kick drum is peaking at 87 Hz, this would mean setting the turnover frequency to 174 Hz or thereabouts. You gessed it, the doubling or halving of a frequency represents an octave in musical terms. You should now have left a fairly narrow band of frequencies coming through. Sometimes I like to add a narrow boost at the peak of where the kickdrum is sitting, though I find this generally sounds better on snare drums than kick drums. Add compression to taste.
Your EQ curve should look something like this, noting that 100 Hz comes up on the EQ graph slightly to the right of the boost at the peak of the kick drum which is of course at 87 Hz:
Step 2 (Top)
Now that we have a nice low kick drum with no pesky high frequencies in the way, it's time to layer this with another kick which will give the required character, click, top end, whatever. Find another sample that you like, bearing in mind it's purpose. Tune this sample to the key you are working in, however tune it an octave above the sub kick. We should now have one heavily EQ'ed kick sitting at 87 Hz (for example) and another sitting an octave above, so at double this frequency. Continuing on from my example in the key of F, this should sit at 174Hz.
We're now going to apply the same type of EQ'ing to this kick drum, but only below the kick. So add a HPF to your top kick drum's EQ at around 87Hz, but importantly we are NOT going to apply a LPF an octave above. Instead we're going to let a lot more of the high end frequencies through rather than just the fundamental frequency. Usually I find setting the LPF's turnover frequency to somewhere in between 12 kHz and 16 kHz is what works the best. With the top kick drum, I generally find that also notching out a few frequencies is also sometimes necessary. I tend to start with 500 Hz, 1 kHz and also 3 kHz which are common problem or simply unpleasant frequencies. Again apply compression to taste, and play around with adding distortion or a bitcrusher which can give the top kick drum some bite if needed.
Your EQ curve should look like the below picture, again noting that 100 Hz comes up slightly to the right of where your starting to attenuate frequencies at 87 Hz, and that we've notched out various frequecies, such as at those at the 1 kHz mark on the right hand side of the EQ graph:
Thats it, we've now got two layered kick drums occupying different areas of the frequency spectrum although with some slight overlap. This gives us the flexibilty to adjust the timbre or sound of the kick drum by playing with the levels of the various layers, or by experimenting with the various amounts of compression and other effects we might want to add, or even by just changing the samples used in each layer.
Now just rinse and repeat the process with your snare drum. Be aware that you will in all likelyhood now be working with higher fundamental frequencies. Your sub snare drum's peak frequency could sit at 174 Hz for example, while your top snare drum's peak may sit at double this, so 349 Hz. It could even be higher. Again you will need to be selective to find a sample that fits well within these frequency ranges. A quick note: I find it useful to tune and audition your drum samples through some or all of this processing. Just as a kick drum sample that sounds great can start to sound odd when you tune it, a kick drum that sounds great without processing can sound horrible when EQ'ed and compressed.
If you want to read more on drum layering, check out Eddie Bazil's book "The Art of Drum Layering" which retails for around AUD $20.00 last time I checked. The same author's "EQ Tips and Tricks" book is a worthwile purchase also.