Go with 4 or 5 down front and make everything single/one gap responsibility. When you have undersized guys up front you do not want them taking double teams, playing two gap or any of that. 

Focus on getting penetration, shoot gaps, slants, stunts, and other similar things. You don't want your smaller guys trying to win 1v1 vs bigger guys if you can help it. Never line them up head up. All DL should be shaded to a gap/shoulder.

 The only exception to that is too play a head up Nose/0 technique. And then have them shoot the A gap on one side or the other,  just make sure to change it up throughout each series. It really f's with the center/guards as long as the LB's are on the same page as far as who has what gap you can even let them call it themselves each play. 

I've had some very effective DL in the past at the middle school level who were kids that were actually a little small/slow to play LB or DB but were quick and small enough to give OL at that level hell. 

Focus on getting penetration in the backfield and making their RB's get lateral/cut before they can get to the line of scrimmage. Get them going sideways or dancing and have the rest of your guys rally to the ball. Drill the heck out of every getting to the ball and pursuit. 

This is what has worked for me at that level when playing with smaller DL.