Yes, I always arrange the songs in a linear way, not only because it's much easier (at least to me), but because I've found that using the "Repeats, codas...." feature don't work well with realtracks (I don't remember the details in this moment, sorry)

The downsides to this are the 255 bar limit and, as Kelso says, printing; let's hope that PG Music will implement XML support in future versions, allowing BIAB to comunicate with other third part notation programs.