There are two things i found especially effective:
1 - put fart towers on the choke between your two "bases", you can fit 2-3 fart towers per side. Upgrade these as fast as you can and place 2 frost traps on both sides of the choke. Slow towers on both sides of the choke are also effective and later on some stun towers behind the fart towers.
2 - you'll find that the above mentioned choke defense will be pretty useful against most of the spawns ... pretty much everything except shielded units. To deal with shielded units you need to place a shitload of fart towers everywhere ... I truly mean everywhere. If you have enough you'll hopefully deplete the shields by the time they reach your choke. This will be very useful against the lvl 40 boss who has huge shield hp.