Ok, when it comes to building a team, if I use Eddie Brock/Peter Parker/Ben Reilly & I plan on converting them to their more powerful alter egos later on in the game, do I pay the points cost of the weaker character only? Could someone explain that to me please?

You only pay the lower cost.

OK, here we go:

You only pay the lower point cost (the one in orange) listed on the character. So, for Peter that's 50 points.

When you swap them in on the orange starting line, assuming you get the chance to actually activate the AE power. You can't switch them in for their Alter-Ego - Spider-man, Venom, etc - until the AE power appears on the dial. It can take some finagaling, but it can be totally worth it in the end.

To help fully explain: You pay the cost of the weaker character only. In this case it would be Peter, Eddie, and Ben. The reason for this is because they are considered the same figure once transformed. So when Peter changes into Spidey you can see that Spidey's dial has two point costs. The 50 is the same as Peter's meaning that Spidey was Alter Egoed into the other points costs mean that it wasn't alter egoed into. Does that help?