Just had a play with Premiere Pro, and I'm probably getting this completely wrong, but the only way I can think of doing this is using 3 layers. If I remember rightly, the players actually go over the logos, rather than underneath it. If you want the logo to go between the players and the pitch, you'll need a static shot of the pitch with no players, then a transparent logo, then "actual footage" of the players - with the layers composed in that order.
I saved the West Ham logo from their website, made a transparant Photoshop image, imported this into premier, changed the opacity setting and added it as a second layer on some footage of a lawn and it looked okay. Thing is, it's over the top of everything - hence the need for that additional layer so that the players themselves go over the logo - but then you'd need them running on around on a prefectly uniformly green pitch so that you could key the pitch out! LOL
Someone must know how do do this so that you can get a Logo to be underneath the players, but above the picth without using a keying? Otherwise, just import a transparent image and put it in a layer above your footage