I'm a long time user and here's what I have discovered to make it work right. The photo you posted looks like the ACW...Automatic Chord Wizard. I've not had problems with the stem splitter but the ACW has been a source of endless frustration and with you saying trying to get it to line up makes me think you're talking about the ACW more so than the stem splitter.

Be sure to set the tempo to 120. You can worry about the actual tempo later. Be sure to set the END or last measure to 120. It starts defaulted at 32 and will stop at that measure. Set it to 120.

I do this the old school way. I listen to the song while looking at the first couple of measures. I guestimate where the first beat of 1 occurs and insert a line there. Often, I'm working with songs that have pickup notes. So it doesn't necessarily equate to the first wave form start being the ONE beat in the song. Move the cursor to where you know the actual ONE beat first occurs. You can zoom in and edit/drag that first Bar Line to get it exactly on the ONE.
Add bar line (L) I then simply start the song playback and tap the "L" key on the first beat of each measure. Once you have all the lines in place you will see what tempo they are. ACW will display the exact tempo in each measure that it has detected. If, for example it is 92 point something..... Now go to the far right to Equalize Tempo, input the tempo of 92, and let it do it's thing. You now have a project that's lined up and will play in time with the BB style at exactly 92 BPM.

Splitting out the stems at this point is a simple matter of going through the steps in the menus. I'm not at the DAW right now but I think it's two or three steps max to get the stems in the utility tracks. You can do the stem splitting before or after running the ACW which I have found to be a confusing process until I figured it out.

Hope this helps.

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