Using SMD and through hole parts for a PCB design you should "mirror" your SMD parts to appear on the solder side. That way you can route traces without using wire jumps or the top layer, provided you find a way to connect them.
If there is no other way than using the top layer to route you might "change layer" and route on top.
Caution: Even if you have planned to use wire jumps you should inform your PCB manufacturer to make the board single sided! PCB manufacturers go by the board design when making the board and if there are traces on the bottom and top layer the result will be a double sided board with plated through holes respectively plated vias.
Post your schematic here and I'll take a close look at it.
Boncuk