Glad you're making progress.
Merging channels should be as easy as mapping them and checking the 'merge services with same name' or whatever the option is called. My experience is that this does not work well, especially with bouquets.
I've got my setup like this;
DVB-S/S2 - four tuners all configured for Sky UK - streaming and recording priority 0 (low)
DVB-T/T2 - four tuners all configured for Freeview from Winter Hill (North West) - streaming and recording priority 10 (high)
For each service from DVB-T that also exists on DVB-S (99% of the channels co-exist) I've manually added the additional service to the channel configuration by opening the channel editor for the specific channel (e.g. BBC One N West) and ensuring both the DVB-S and DVB-T variant are checked).
As soon as you add a DVB-T service to a DVB-S channel thats managed via bouquets - the channel number will automatically change to something else (normally in the 4000 range on my system) and will need to be changed back manually.
I also had to uncheck the 'Always use the name defined by the network' flag or else TVHeadend would split out the DVB-T and DVB-S services as sometimes they don't match (using the BBC 1 example again, on Freeview it's named 'BBC ONE N West' and on satellite it's called 'BBC One N West' (notice the different caps) - TVHeadend see's these as different names and splits the channels up for some reason).
Apart from that it's easy :)
The streaming/recording priority (defined at the adapter level) tells TVHeadend to prefer the DVB-T tuner over the DVB-S tuner if I try to watch/record something that exists on both Freeview and Sky - the reason being, I keep the DVB-S tuner free to record encrypted channels.
p.s. not sure if you know this but TVHeadend can stream multiple services from the same mux so if you try to watch two channels (or watch one and record one) from the same mux, it uses just the single tuner which is nice :) On Freeview, the five main channels exist in HD form on a single multiplex so that means you can essentially record/watch as many streams from those 5 channels as your hardware can handle whilst using only a single tuner on your DVB card. The same applies to the DVB-S card too but the satellite multiplexes are not organised as nicely as the Freeview ones :)