If you are invoiced by John Smith that is who the cheque should be made payable to. If you are invoiced by JS Holdings Ltd., that is who the cheque should be made payable to.
It doesn't matter that you know John Smith owns JS Holdings Ltd. If you are receiving invoices from two separate entities you should make your cheques payable to the appropriate one.
It may well be that John Smith has a very good reason for working under two separate businesses and you should pay him appropriately.
Just to give you an example, I am involved in 3 businesses. My accounting practice is a Proprietorship, my wife and I jointly own a Partnership and we are both Shareholders/Directors of a Limited Company. I would not like to see invoices sent out by my accounting practice paid to the Company.
Sorry I can't help you with the GST question - I don't think it is possible to allocate a percentage of the GST paid to one account and the balance to another - but maybe someone who is more experienced in Simply can help you.