You can align the bikes any way they fit on the trailer, the important things to consider are:
- ease of loading / unloading (not such a big problem with bikes this size)
- load so you have sufficient tongue weight and even weight distribution
- trailer capacity
- strapping point locations
Most small motorcycles require about 6' of trailer space in length and about 3' of space between the tires of the bikes. This means you could get 2 small bikes side by-side in a 6x4 platform which is about as small a trailer as you can find.
3 bikes can be loaded on a 4x8 platform, the outside bikes facing forward Loaded first), and the middle bike facing backward, (loaded last).
You could also load them on 45-degree angle, to get a little more separation between bikes -- that's a lot more work and strapping complication for not much benefit.
My concern would be the trailer holding up. Trailer capacity is one thing, evenly distributing 1200lbs of drywall puts 12.5lbs/sq' of pressure on the deck - a motorcycle tire has a small contact area -- is a few hundred times greater. I won't get into the physics, but rolling over a rough rail crossing can destroy a lightweight trailer that's loaded to capacity with motorcycles - particularly a bolt together platform type as they lack the rigidity of a welded trailer with sides.
If it's the trailer you pulled to my shop, I'd limit it at 2 bikes.
A couple of other tips:
- Never transport on the center stand
- Use the sidestand and tires if you can, particularly with bigger bikes, if not balance vertically with straps
- leave bikes in 1st gear,
- drop tire pressure to 15psi on the bikes, 30psi on the trailer tires.
- pull the suspension down 1/2 it's travel with the straps.