Bottom line: Personal preference.
The uncrossed string arrangement allows each hand full access to all positions on the string set without interference. In the uncrossed arrangement, you place the left hand's string set (normally the bass strings) to the player's left, and you place the right hand's string set (normally the melody/guitar) closer to the player's head. The left hand plays the bass strings just as on a 6 string bass. The right hand plays the melody strings from the right, allowing for full access to both string sets. Good for smaller hands. Some say better for beginners. Preferred by many musicians. Uncrossed Bass Bottom tuning feels natural to standard guitar and bass players because the strings are in all the familiar places.
The crossed string arrangement, where in the normal playing position the musician finds the lowest strings nearest to his head and the highest-pitched strings furthest to his left, is just as common. This arrangement means that when your left hand is playing bass strings around fret 7, your right hand is blocked from playing melody strings at that same place. Better for larger hands as your hands will have to reach across the fretboard with fingers more outstretched. Chapman Stick instruments use predominantly crossed tunings.
Other considerations and random thoughts on the subject:
FIrst off, what tuning are you using?
Bass bottom/straight 4ths tuning can be crossed or uncrossed and/or mirrored.
Most Chapman Stick style tunings are going to to be based on a crossed hands setup.
If you choose crossed hands stick learning materials and techniques can be used.
If you are an existing bass or guitar player who uses some tapping or touch techniques and wants to expand that potential, your probably going to like uncrossed hands. It will feel more natural to you at first.
If your new to touchstyle and not stick-centric but rather just exploring and enjoying the ride then probably bass bottom/ 4ths tuning will be easier to navigate. While uncrossed hands will be more like what you are used to if you have any experience with bass or guitar playing.
If you are a bass player, you for sure should go with bass bottom/4ths tuning. As for crossed vs. uncrossed, it’s a matter of personal taste. Try to experiment with or at least simulate the different string arrangements and see how it feels. Think about what sort of music you are planning to make with your megatar and imagine how it would best work for your hands?
If you see the instrument as a monster 12 string bass, then bass bottom tuning with crossed hands gives you what you need. Like having a bass that goes from a low B on the bass to the upper range of a guitar, and plenty of strings to work with.