There are no stupid questions... just stupid answers... and I'll attempt one now... (oops if you read my reply prior to 09:35 just ignore it... Melanie must remember to read the damn Datasheet before giving advice!!!!!!!!)...

TMR1 DOES have a crystal input capability.

You can have a CRYSTAL which requires loading Capacitors (connected as per the Datasheet schematic), or you can use a RESONATOR - the three pin types are neat because the middle pin is connected to Ov (Vss) and the outer pins connect to your OSC pins (polarity irrelevant). On those Resonators, the Capacitors are built-in and you don't need any further components.

You can have any (hopefully) square-wave input as a Counter for TMR1. Any external circuit that is giving pulses... (you want for eample TMR1 to tick at exactly 1Hz, then you can feed it from the output of a DS1307). Yes, you can feed-back a PWM signal as an external counting source for TMR1, but it's too early in the morning and I've had insufficient coffee to attempt to guess why you would want to do this.