What scale length and what do you want to tune the strings to?
Scale length will be either 30" or 34". I no very little about bass guitars, but I am looking to tune for a deep rich sound like biues music. Its only going to be 2 of the strings, I just wondered which 2 String 1 and 2 or 3 and 4. I was thinking that 3 and 4 would be the deepest tone, but like I said I don't know much about bass guitars.
Oh, I thought you were asking which string gauges to use. That would be a technical question so, as a builder, I could answer that given the scale length and desired pitch. You're asking what pitch to tune to and that's a musical question better answered by an actual musician.
But since you only have two strings you probably need to consider what keys you are going to be playing in most and then choose your tuning based on that. You're right though, thicker string, deeper tone.
The one I made used the 3 and 4 strings from a Fender jazz set which are smaller than normal bass strings. It is a regular cigar box with a long stick thru design. It sounds nice and 'bassy' but it is not nearly the volume and fullness of a regular bass due to the size of the box. I don't really play bass but it is fun to mess around with. If you got a full set it would be easy to experiment with the strings.
as a bass player, I would suggest a 2 stringer use the #4 (E) and #3(A), that's where I spend 75% of my time on a 4 string.
Thanks everyone for your quick response.