For connecting top layer tracks to the bottom layer with home made boards i add dedicated holes for that purpose and solder a wire in.
You can sometimes get away with using the holes for top/bottom joins AND components, ie, if you had a resistor laying flat on the pcb you can solder both sides easy and the resistor leg itself joins your tracks.
However you have to carefully watch what you're doing if you go down that road, lots of components cover up the holes, relays etc. so you can't solder both sides. You dont want to find that out after youve made the pcb.
So yeah, i just have dedicated holes for joining the top/bottom. It gets around the whole issue of keeping track of which holes can and cant be soldered on both sides.
But i do agree with what other people have said, making two layers boards at home is pushing it.
It's so much nicer to have them made professionally.
Ya really dont understand how nice it is until you actually have some pcbs made professionally.
The day they arrive and you have your board design in your hands with mask and silkscreen is a pretty nice feeling. And wow is it nice to assemble them when the holes are correctly aligned and you have a solder mask