Unless you state/know the orientation of gene you have cloned into a vector, there is no way anyone can advise you which end you need to cut to produce a cRNA.

If you are sequencing the plasmid and using Blast, you should very easily see the orientation of your gene in relation to the vector, as long as a portion of the vector is sequenced with your primer.

Best, 

My thinking is that the sequence generated from the M13R primer came up in the blast search as plus/minus. I interpreted this as the m13R primer is sequencing the antisense strand (the fragment went in backwards with respect to the vector orientation). Thus, synthesizing using the T3RNAP would make antisense sequence. I don't know if these assumptions are correct though.

You should be able to tell very easily by looking at the alignment with your gene - either the sequence generated using M13R will show the sense strand or the antisense. It can never be both!

[I am assuming that you have picked single colonies cleanly. In case if you used blunt en ligation or a single restriction site for insertion, both orientations are possible. However, if you mixed the two colonies before DNa preparation, your sequence profile will show overlapping peaks and would give you a very limited and unusable read - which I imagine did not happen.]