6% isn't "too high" in terms of market rates at the moment, however it's a very subjective question whether it's too high for you. The real question to determine is if paying 6%, can you make more than 6% return (to cover the costs plus your profit)?
As for a rule of thumb, there's none I know of, however your best bet is to take the time to model it in Excel (not difficult). It's different for each portfolio or investment. Something with a high standard deviation of returns is already high risk, adding margin to it only makes it worse. So, long story short is that, "it depends".
Okay so we are assuming that you can sustain 6% or more return on your investments.
Personally I would compare that rate to what lines of credit are going for and do what ever is least expensive.
Either way your risk is the same. Your net worth is the same. Your assets will be the same.Your liabilities will be the same.
Its just a matter of who you owe it to and what the rate is.
Don't be afraid of having a second mortgage. If the stocks go down either way you have to sell what's left and pay your debt.
Or what I should maybe say is don't be more afraid of a line of credit more than margin in your investment account.
That seems a little high in my experience. I've used a home equity line of credit instead, as the rates are much lower (~3.5%).