You are probably referring to "prime" or vendor managers (some of whom also operate their own agency and their own travelers). Vendor management is essentially the hospital outsourcing human resources to create a service with an exclusive contract that manages subcontracting agencies. It is a real pain for hospitals to manage 30 agencies, all with different contracts. Just like outsourcing just about anything, it can lead to better efficiency and lowered costs for hospitals.
There are pluses and minuses for travelers (and agencies). One minus is that your agency no longer has a direct relationship with the hospital, or direct contact in many cases. That can cause communications issues as you have experienced. But it also reduces a lot of noise. Pluses are a uniform hospital>vendor manager>agency contract with all agencies getting the same bill rate. This means when you shop around for this specific assignment, you will learn what agency actually pays the most out of the same bill rate. That is useful if you find the agency otherwise valuable to work for, you can prioritize taking assignments with them knowing they are better paying than others.
Most vendor management contracts prohibit subcontracting from one agency to another. As the traveler, you are two steps removed from the hospital in the usual scenario you are in: hospital>vendor manager>your agency>you. So I'm not understanding how there was yet another agency involved.
But yes, your only point of communication (like normal) is the agency you are contracted with. Once you have interviewed with a manager (which is sometimes skipped in VM situation), hopefully they have encouraged you to reach out should you have further questions and shared a contact number, and of course when you actually start, you can talk directly to the hospital.
By the way, agencies also outsource. That outsourcing can include office services, recruiting and marketing, payroll, housing, and benefits. Even contracts with hospitals - get yourself a three contracts with vendor managers and you now have access to a wide variety of jobs without having to manage and keep up with openings at hundreds to thousands of hospitals. Outsource independent recruiters working at home and sit back and skim whatever money from the bill rate is left over. In the extreme, a one man agency with dozens of travelers!