Viruses that possess more than one type of symbol may reproduce on more than one type of cell.
Is the reproduction rate related to the complexity of the virus?
Yes. Initially I thought it would be related only to the stats and/or abilities but using the complexity of the shapes makes it more interesting since you can recognize viruses that are more complex and more dangerous.
Movement: Should the viruses be controlled like a normal RTS by selecting and moving or should I go for a different movement scheme like positioning colored markers to move all viruses of the same color to the position of the markers?
Hmm. What about the option of giving orders to each cell along the lines of (be aggressive/reproduce/do nothing)? And let them figure out things themselves.
All of the various entities do look quite large: is it a case that there's going to be a lot of scrolling about involved when you're playing the game?
Yes, it would be possible to give orders for each type of virus chosen by the player. I would certainly play it like that too.
About the scrolling and the entity sizes, the player will be able to control the zoom and hopefully he will be able to easily scroll around the map by using the mouse or the arrows keys. I'm finishing map generation and then I'll start playing with map sizes to discover what feels best.