You either will have to have the income to support both debts or the investment property produces verifiable income for the past two years that you can use to off set the debt. If this is the case, then you should not have a problem qualifying for both.
I would advise going to separate residential lender and commercial lender. Most of the residential lender do not specialize in commercial and will try to take on your deal and co-broker it out. You will be able to get a better deal and service if you use two lenders.
In the case that both properties are residential, then you can use one lender. Be sure to negotiate your closing cost as the lender will have less work since most of your info that is in one file can be transfer to the new one.
The fact that it is a Fsbo has no bearing on the deal. You will need a purchase agreement, which you can have a local agent draft it for you or a real estate lawyer. I would not advise using a template one unless you know what you're doing.