Try: "I would like to rent a two bedroom apartment furnished with a twin bed in each, please." Or: "Would you help me find a two bedroom apartment that is furnished with a twin bed in each?"

Could you please arrange an apartment with two bedrooms, each containing two twin beds? Does it have to be one sentence? It's kind of complicated. I suggest something more like: Could you please help arrange an apartment? It should have two bedrooms with two twin beds in each.

Absolutely correct. You may want to clarify by saying "two bedrooms with twin beds in each room." That is the only addition I can think of for this sentence.