How many hardware timers are there on the ATmega328, do you know? I would need maybe 5 different timers.
The Atmega 168/328 has two 8 bit timers and one 16 bit timer.
As I said though, it's possible to use a single timer for multiple purposes, even to provide timing for 5 separate signals.
Well, Yes and No. For your purposes, you don't need nearly so complex an implementation. Googling state machine tutorial should provide some useful links, this looks like a potentially good start (I just skimmed through it myself): http://www.generation5.org/content/2003/FSM_Tutorial.asp
You'd be looking at a very simple state machine, with two states and two events. The states being Signal On, and Signal Off, and the events being Turn On, and Turn Off.
I would start with an implementation utilizing the Blink Without Delay method of timing, and only look at switching to a timer based implementation if you aren't getting the accuracy you need.