RF remote and best setup to control IR devices from afar

The best remote is the one that best fits your needs and requirements within your budget. No need to recommend a touchscreen remote if you want hard buttons and vice-versa. The bottom end for cost with RF remotes would be the AVL-300 or using a "Next Generation" Extender with your current remote. Then you have the Harmony 890, 900, and 1x00. Up another notch are URC RF solutions such as the MX-880, 980, 5000, and 6000 with a RF base station.

As for how to best control the IR devices across the house with an RF remote. I'd use RF

If you are saying that it is very far away across the house then a typical entry level Harmony RF remote might not cut it due to the range. With something like a URC MRF-350 you can put the RF antenna away from the RF base to increase your range. You can also add additional RF antennas as needed. These antennas however have to be wired to the RF base using a standard cable or something like CAT5.

Yes you are missing something. RF universal remotes only communicate with their RF to IR base/extender. RF universal remotes will not control RF devices other than their extender. You can't control your RF ceiling fan since RF universal remotes can't learn and don't have an RF device database.

For a RF universal remote to work your devices must be IR (or possibly RS232). There are very few exceptions to this, such as one remote that can control a DirecTV DVR in RF mode and another that has the PS3 Bluetooth commands built in.

An RF universal remote has two parts. The remote which transmits IR like a regular remote or RF and the extender which receives RF and transmits IR. You put the extender with your components and it flashes IR using stick-on emitters or flashers that need line-of-sight to your devices (the Harmony 900 is an example of this).

Yes, you can send a combination of IR and RF from the remote. In the setup you assign each device to be controlled by either IR from the remote or IR from the extender (which is RF from the remote).

What you are talking about is what Harmony refers to as an Activity such as Watch TV.