It is probably better to use a colorspace aligner, as they accommodate sequencing errors better than if you transform the reads to basespace and then map - due to the nature of solid sequencing, when converting from colorspace to basespace, a sequencing error will propagate down to the end of the read.

I recently used CUSHAW3 with good results. Bowtie (but not Bowtie2) and MOSAIK can also align directly colorspace reads.