Even if you are traveling on a foreign passport, you remain a US citizen, and the US will still consider that you are subject to any restrictions it has placed on its citizens regarding travel to Cuba or indeed any other matter.
US citizens are required by law to use their US passports to enter the country.
There is no penalty for violating this law, but you will raise all sorts of red flags if you show up with a Filipino passport without a visa in it. You will not be able to get a US visa in your Filipino passport because you are a US citizen. You will therefore need to show your US passport to board the plane for the US, and, of course, at the US immigration desk.
Would I just buy the ticket using my Filipino passport?
You can do that, yes. You can show your Filipino passport in Cuba.
What kind of documentation/proof would I need to return back to the US?
You will need your US passport to return to the US.
And as a US citizen travelling with a foreign passport, where would I go for US customs?
You can go to the US citizens line, because you will be traveling with your US passport.
One strategy you could use would be to book two round trips. The first is to Mexico, Canada, or some other country. The second is from that country to Cuba. More information about this approach is available on this site at I have two passports/nationalities. How do I use them when I travel?; it is covered in the accepted answer under the heading Case 3: Same name, dual citizenship not OK.
To reiterate: traveling with your Filipino passport will not protect you from any action the US may pursue against you for violating its laws.