Hi @thormj,
I'm not sure if I'm following you 100%, but if you want to load the top layer as the solder paste layer, you can just rename the file
Top Layer files are expected to end in *.GTL,
Paste files are expected to end in *.GTP
Since all the gerbers are formatted the same way, it is possible to trick the V-One software and load any layer as a top or paste layer.