One of the company's co-founders is investing and to avoid high fees I suggested we use our merchant account whereby he will make a payment online and then I will receive the money in the UK. Is this common? Are there any tax implications - as in do we have to list that as a sale?
I am not sure about the tax consequences however you will end up paying 2.x% depending on the card in question if you use your Merchant account.
If the amount comes in as a wire transfer you will pay between 25$ - 50$ in bank processing fees. If the investment amount is less than a US 1,000 it may make sense to do a credit card payment. But if it is any larger it may be better to receive the payment through your bank account.
I am also not familiar with UK tax laws but I would presume that you could mark the receipt as investment of capital rather than revenues both when you receive it and when the investor makes the payment. It must show under that heading on his account statement and your merchant account receipt.