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.
I am glad you're here! I see you are working late, as am I. I would recommend speaking to a Lender for sound advice. You will receive lots of good advice from Realtors on here but you are in need of help with finances. You may want to speak to a couple different companies and see who you feel comfortable with, and who can provide the best rates.
I recommend speaking to Michigan United Mortgage MUM. They are a Michigan company and the nicest hardest working individuals I know. http://mumloans.com/
If you would like a number for a direct contact you can contact me via trulia or confidentially by following the link on my web page and I can provide that for you.
Just for your protection who is handling the contracts and title work for the FSBO you bought?