Using Flexisign for spot colour work shouldn't be too much trouble and I'm pretty sure it works in a similar way to Signlab but will need to be vector. If your original shape is vector no problem choose the colours you want and then either separate them to a laser printer using laser film (I use Delta film from Autotype) wipe over with white spirit or an image enhancer, I find that warming slightly makes the image far blacker, expose your screen as normal. If the solids are too big and your can't do the screen successfully, cut the shapes but instead of vinyl use Ruby film. I'm sure Flexi has a 'cut by colour' function as well as a 'registration mark' function. Sign programmes usually have some good weld routines allowing overlaps to be extended slightly only where they overlap, this is great for any slight miss-registration.
Alan