You are right, it is a little more challenging to transition from one technique to the other in the sitting position. This position lends itself more to therapeutic work than to a gracefully flowing massage. As long as you make sure that you provide good support it will feel fine, especially when people have a hard time sitting cross-legged with a straight back. You can make up for that to some degree by providing good support. The biggest problem I always see here in Thailand is that therapists do not support the back and then it all feels wobbly and collapsed. But from what you wrote, you have it figured out.