Perhaps this is my lack of formal musical training here, but I'm having a hard time understanding why Sonar always calculates tempos in terms of quarter notes. I'm working on a project in 6/8 time at a tempo of 104 eighth notes (or beats) per minute, but in order for Sonar to play at that speed, I have to set the bpm to 52. 
 
But my understanding is that in a time signature, the lower numeral is the beat unit, which in the case of 6/8 is an eighth note. So surely, for "bpm" to actually mean beats per minute, it should be a measure of how many beats are in a minute, a beat being defined as the lower numeral in the time signature. 
 
Cue a real musician to tell me why I'm wrong 

Your not wrong that is just the way sonar does it. However with written music 6/8 is often counted and conducted in 2 not 6 beats. In the case of counting is 2 the tempo is applied to the dotted quarter and will be clearly noted in the music.

I guess the beat division of 6/8 time depends on the tempo...if it's a fast tempo then the beat is usually felt as two dotted quarters, but if it's a slow 6/8 then the beat is usually counted as eighth notes. I would have thought, however, that a professional music program like Sonar would either define beat strictly as the lower numeral in the signature, or at least giving the option of how to define the beat in terms of the bpm. It matters a lot when you're using a drum machine for instance. 

I found that exact same thing recently when playing in a midi drum part for Metallica's "Nothing Else Matters". The music score clearly states the tempo at 96 (IIRC) in 6/8. So I bang those numbers in to find everything completely out. I actually changed the time sig to 2/4 to correct it. I didn't think to halve the tempo as I would have much prefered to hear the metronome playing 8th notes as opposed to 2x1/4.

Weird!

Luckily I had enough theory background to do something, about it, even if I went about it in a round about way.

STinGA
I found that exact same thing recently when playing in a midi drum part for Metallica's "Nothing Else Matters". The music score clearly states the tempo at 96 (IIRC) in 6/8. So I bang those numbers in to find everything completely out. I actually changed the time sig to 2/4 to correct it. I didn't think to halve the tempo as I would have much prefered to hear the metronome playing 8th notes as opposed to 2x1/4.

Weird!

Luckily I had enough theory background to do something, about it, even if I went about it in a round about way.

So the score's tempo of 96 is based on what, 96 dotted eighth notes per minute? I just listened to the song on YouTube along with a metronome clicking away at 4/4 in Sonar, and at 96bpm there are 4 clicks of the metronome for every bar of 6/8 in the song, which means the metronome is clicking at dotted eighths, right? But why on earth would a 6/8 song's tempo be expressed in terms of dotted eighths? I'm really confused now. 

 
 
In my experience (I transcribed lead sheets for music publishers in my younger days) when I placed a BPM at the top of the manuscript I would always write the note that was equivalent to one beat.
 
 
 
Even when it's obvious it still seems like a good practice; If you are basing your BPM on a eighth note, then place an eighth note with an equal sign next to the BPM.
 
 
As mentioned, If you are in 6/8 time and the BPM is based on two beats per measure than a dotted quarter note should be placed next to the BPM.
 
 
I've seen sheet music in cut time with a BPM of 85. No indication that a half note represented each beat. In this case it was obvious but why not make it perfectly clear?
 
 
As far as 'Nothing Else Matters' if I were writing that lead sheet today I would use a dotted quarter note with an equal sign and a BPM of 48.
 

You are correct.  Just a note, thought, that by convention, people often count the 8th notes at slow tempos and count the larger divisions at fast tempos for both 6/8 and 12/8.  For example, if you have fast triplets in 12/8 people will usually count 1-2-3-4 with a triplet for each count because it is too hard to count otherwise.
 
You are still correct, though.
 
>>Do you think that maybe Sonar's idea was to keep consistency based on clock ticks?  For example, the ticks are by quarter, so maybe the developers felt it would be more confusing to have the number of ticks change every time someone changed time signatures, especially since a single song can change time signatures many times.

or try doing something in 7/8 and having to remember this:
 
In some projects you may need a different timebase. For example, if you wanted to use eighth-note septuplets (7 eighth notes per quarter note) and represent them accurately, you would need to have a timebase that is divisible by 7, such as 168PPQ. SONAR uses the timebase you choose for a project to determine the range of tick values in the Now time.
http://www.cakewalk.com/Documentation/default.aspx?Doc=SONAR%20X2&Lang=EN&Req=Recording.09.html

It sounds to me it is the way Sonar is handling time signatures and it is probably more complex than it should be. I can give you some insight as to how Studio One handles time signatures.
 
Firstly the tick resolution or pulses per quarter note should not have anything to do with it and that is the case with Studio One that is for sure.
 
Putting my metronome into 6/8 creates 6 eighth note clicks per bar and at the right BPM of 104 as sharke mentions in his OP. The first one can be accented or have a different sound too which is handy.
 
If I put my time sig into say 7/8 or 9/8 I hear the same thing 7 or 9 eighth note clicks per bar with the first one accented. If I set 12/8 at 120 BPM I hear all twelve clicks per bar so I really get the triplet thing. It is silly to not hear the subdivisions. They are there for a reason. You can still feel it or count it any way you want but the actual number of audible metronome clicks is directly related to the number set in the top part of the time sig. That to me seems like the right way to do it.

cubase handles timing pretty much the same as sonar.  this is a good vid to measure the timing with...
 
http://upload.wikimedia.org/wikipedia/commons/e/ee/Video_of_6o8_at_90_bpm.ogv