I have a second router(one I purchased from best buy) attached to the ISP's default router (one they provided)
Can the ISP see what I download off of the second router? Or can they only directly see what goes through their router?
I am assuming all your home devices are connected to the Best Buy router you purchased. Any files/data/streams/websites accessed from the internet will flow to and from the internet, to the ISP router, to your router, to your device. This means the ISP can potentially see everything you do on the internet. However, this does not mean they can, or even try to.
They can see where you connect, unless you route through a VPN - in which case all traffic would appear to route only to the VPN.
Whether they can see what you do as opposed to where you do it is dependant on the connection being secure [HTTPS]. At the least, they can still see how much data is transmitted from which address.
The added router is not any additional layer of security, it is merely another node on the route.
There are three different levels of information that an ISP might know (for data passing through their router):
The server address that you are retrieving information from. For example, 188.8.131.52 is one of the server addresses that serves google.com. A server address can be associated with multiple websites or services (but not always, especially for large services). Typically, unless you use a VPN, an ISP will have access to this information.
The domain name you are requesting. For example, google.com If you use the ISP's DNS (e.g., a phone book for domain names -> addresses), then the ISP will have that information. If you use a service like 184.108.40.206 as a DNS, then the ISP will not have that information. Mind you, it may be easy to associate the address with the domain.
The actual data you transmit. If you are connected using HTTPS and have not ignored any security warnings in your browser, you can be relatively confident that the ISP does not have access to this information.
If your question is: will my local data (e.g., data between computers are your home) be seen by the ISP then the answer is (probably) no.