It really doesn't matter at what point you connect what to what. I think our house is living proof. Our outside line comes in, is hard wired to a jack on the other side of the wall, that jack hardwires to a three way splitter, a filter put on each end. One part of the now filtered splitoff goes into a 6 way splitter for multiple phones, answering machines, and receivers. The other split goes 25 ft down to two more phones and one more receiver. The third split goes 150 feet to an 8 way distribution block that includes phones, answering machines, receivers, and the modem. It all works just fine.. I figure if we don't fuck with it, it won't fuck with us 😛
So yeah.. just hook it up however is more convenient..
EDIT: I almost forgot to mention. Our router sits with our modem. Our server is back where our phone line originates. Since wireless wont reach that far reliably, we run a 150ft run of RJ-45 from our router *outside* all the way back to a switch in the room with the server. From the 5 port switch it makes connections to the server, a desktop, any test systems running, and our laptops when we're working on things in there. Again, things work perfectly. So we use the extremes of both of your questions. You really won't have a problem.