Being fairly new to drumming and vintage kits, I had the same question you have just a few weeks ago. I was tuning a drum set for the first time and did not really know where to start. My 50's Kent bass has the original calf skin heads so I did not want to change to new heads or do anything radical or damaging. Here is the gist of a response I got from a more-experienced drummer:

What kind of music or style do you play? If you play jazz or musical styles with less emphasis on the bass drum as a timekeeper, resonance is a good thing. A good number of jazzers keep the resonance for full effect and tune their bass drum like a big tom drum with the lowest pitch (or second lowest pitch if you want your 16" floor tom to be lower than an 18" bass drum). To some degree, the same way of looking at the bass may be true for styles of old country and early rock'n'roll. Your method of tuning the two heads relative to each other (equal tuning on each head, batter higher than resonant, resonant higher than batter, etc.) along with your method of tuning an individual head (tuned high to the point of being choked, batter tuned low to the point of flapping, etc.) can affect the amount and the character of the overall resonance. If you want a good amount of resonance but need to control it better, there are several websites I ran across that can direct you how to tune a bass drum like a tom for the resonance you want.

If you are going the route of pop, rock and more modern music (which it sounds like you might be doing), the bass as a thumping timekeeper is more important. The Powerstroke 3 series of heads were recommended to me for the tight, modern bass drum sound.

To keep the original heads and cut resonance, there are several options. You can use the tried-and-true method of a quilt/pillow/foam in the drum or touching the head(s) to limit resonance. Similar effects can be accomplished with muffling attachments that touch the head(s). They also make heads that have adjustable muting and muffling built in (I think Evans makes them?). This muffling method has the benefits of being relatively adjustable, non-destructive and non-permanent. Another method to cut resonance is to extremely detune the resonant head or, even better, take the resonant head off of the bass drum to restrict the source of the sound to the batter head. This method has the same benefits of pillows/quilts/mufflers although is not quite to easy to adjust on the fly. Instant 1970's "cardboard box" sound if you take the front head off. A third method to cut resonance is to cut one or more port holes in the resonant head. The placement and size of the hole affects how and how much the resonance is cut. Both Aquarius and Remo make port-hole kits if you want to do this yourself. This method offers the additional benefit of easy mic placement for studio work but has the disadvantage of being destructive and permanent for the head. Maybe not the best option with original heads if you want to keep them. If you are aiming for that tight, thumping rock bass sound, keep in mind you will lose some volume and fullness that comes with resonance.

There are probably a million other ways to limit resonance but this was some of the advice I was given. I went the jazz route for now and have my bass drum set as the lowest-pitched tom drum with both calf skin heads tuned equal pitch. As I noted, I am relatively new to this drumming thing (playing guitars and other stuff for most of my life) so I hope somebody will chime in and correct me if I do not have a clue what I am saying. :) Good luck!

An old trick (probably not a great idea if the drum is miked) is to loosen the top two tension rods on the batter side.

It's a quick and convenient way to get a flatter sound if you need to change sounds during a set and it could well fix your overtone situation.