If we have a SAQ A compliant website for online signups, can we also use SAQ C-VT for phone orders? I'm thinking yes since they're separate payment channels but this aspect is new to me.
There is a relevant FAQ from the PCI SSC that addresses this questions. The gist of it is that you if the environment meets the criteria for the SAQ then you can use that SAQ as a reference for the requirements you need to meet for that environment.
In practice you would complete SAQ D and evaluate your responses based on how they pertain to the two environments. Each legal entity should only complete one SAQ or ROC for the entire company. To complete multiple SAQs would be misleading, as you can't answer truthfully to all criteria needed to complete either the SAQ A or C-VT, as the requirements for doing so apply to the company as a whole, and all SAQs besides D have stipulations that there are no other cardholder data flows.
When conducting your review, if neither SAQ A or SAQ C-VT contain a particular requirement, meaning the PCI SSC has deemed it not applicable for a particular type of environment, you can mark it as N/A in the SAQ D you are completing. If either one of them contain the requirement then you should evaluate how you are meeting that requirement for the related environment and document it accordingly.
The key to this method, as it states in the FAQ, is clearly documenting and explaining the approach you are taking in the Executive Summary of the SAQ. You need to clearly document and explain how the two environments are separate and individually qualify for a given SAQ, and the approach for evaluating each requirement for compliance.
Yes - it is fine to use two SAQs, one for each acceptance channel iff there is no connectivity between the two channels - ie there is nothing that is 'connected to' both channels. It is wise to let your processor/acquirer know that this is your approach and to document this in the SAQ.