I struggle with this every time.  Why is this so difficult?
 
Obviously a result of poor-potty-training?
 
Can anybody give me some love?
 
If you know how to do this, please provide some guidance to this poor wanting soul.
 
I have a clip that is yearning to fill 2 bars.  http://logicalarts.com/music/beeps0514a.wav
 
I want to set the tempo to a particular pattern.
 
Four beeps in each sequence.
 
I want to set the project tempo to:
 
Measure one:
beat 1 =  1st beep  pattern 1
beat 2 =  4th beep  pattern 1
 
beat 3 =  1st beep  pattern 2
beat 4 =  4th beep  pattern 2

Measure two:
beat 1 =  1st beep  pattern 3
beat 2 =  4th beep  pattern 3
 
beat 3 =  1st beep  pattern 4
beat 4 =  4th beep  pattern 4
 
 

For something like that I'd use Project Menu--->"Set Measure/Beat at Now".
 
In your instance 
 
Measure one:
beat 1 =  1st beep  pattern 1 ->Move now time to this beep press "Shift+M" - Set to Measure One - Beat 1
beat 2 =  4th beep  pattern 1 ->Move now time to this beep press "Shift+M" - Set to Measure One - Beat 2
 
Repeat as required...
 
HTH

If you trying to set a relatively constant tempo that will give you that alignment, it's not going to happen. I checked out the clip, and if you trim and drag it to bring the first beep back to 1:01:000, and then set the first beep of the third group to be 2:01:000, you get an average tempo of about 128BPM. But the time between the first and fourth beeps of a group and from there to the first beep of the next group is not the same so you end up with alternating tempos of roughly 156.5, and 107. I doubt that's what you want.
 
I suggest you trim, drag and set the first beat of the third group as described (don't try to set 1:01 in any case; that's not possible and not needed), and I think you'll have what you want at a tempo just a hair over 128. In fact, it's close enough that you could just set the project to 128 to begin with if you're only going to use one iteration of the alarm loop.