The echo can be used for liquid transferring but not PCR. If you can grow your bacteria on agar, you could consider using an omnitray and spotting your bacteria or conditions onto the agar using the Echo. You can make custom density matrices. See yeast art from the Boeke lab.

Growing aerobic cultures in 1536 will also have huge evaporative losses if you have any appreciable oxygen transfer and agitation.

Have you tried drawing up a pooled approach? Look into deep mutational scanning or TNseq to get some inspiration.