If you intend on using a ring wall foundation (ie. no deep foundation elements) then there is generally no need to remove the cobbles or boulders. Excavate the cobbles that will interfere with the foundation and make sure the subgrade passes a proof roll. This is assuming that you are dealing with an alluvium or colluvium. However, if this is a non-engineered fill then you are best to remove it all.
From the design standpoint throw out the CPT tip values that hit cobbles and all SPT refusals, using only values that represent the sand. Your design should be based upon the silty sand density and phi, ignoring the effects of boulders.