How do I account for the capital cost of the digester?

If the digester has a long lifetime, you can probably assume it will not require replacement during the project lifetime.  So you don't have to specify its replacement cost, just its capital cost and O&M cost.  To do that, you could use the system fixed capital and O&M variables on the Economics window.  These are variables that account for the cost of any pieces of the system not accounted for elsewhere.  The system fixed costs apply regardless of the system configuration, so this approach will work only if all systems you are modeling include the digester, and you are considering only one size of digester.

You could instead include the capital cost of the digester in the capital cost of the generator, but you're right not to mix the O&M costs of the generator and the digester since one is in $/hr and one is in $/yr.  If you could express the digester O&M cost in terms of $/kg of biomass feedstock consumed, then you could include the digester O&M in the biomass feedstock cost.