I don't know of any search tool that would be perfectly capable of both. Wheretocredit.com has a calculator. There you can enter the segments and booking classes and it'll tell you how much you'd earn in all FFPs. The ITA Matrix is also helpful since it gives you the total distance of your flights, once you know how many EuroBonus miles a booking class on a given airline gives, you can do the math yourself (this is a little less convenient though).
Personally (I'm collecting with Miles+Bonus), I have a pretty good idea which airlines give many miles in a given class and which ones don't. Then I use the matrix to see which flights are cheap. Combining both I arrive at what to book.