Sorry if this seems a stupid question ...Do I have to bid on Ebay as well as using Myibidder (i.e do I have to set the same max bid on Ebay that I set in Myibidder) ?

No, you don't need to place your manual bid on eBay. Setting a snipe with Myibidder is enough.

The only exception is when you suspect the seller may blocked you so you want to check that your bid can be placed. This way you place a minimum manual bid first just to make sure.