In v6, you can create CNAMEs via Settings | Local DNS Records (just as in v5).
As Introducing Pi-hole v6 mentions, Pi-hole v6 consolidates v5's multiple settings files into a single, richly commented file, /etc/pihole/pihole.toml.
You can add your CNAME definitions to that file to the dns.cnameRecords section, e.g. like:
# List of CNAME records which indicate that <cname> is really <target>. If the <TTL> is
# given, it overwrites the value of local-ttl
#
# Possible values are:
# Array of CNAMEs each on in one of the following forms: "<cname>,<target>[,<TTL>]"
cnameRecords = [
"time.fritz.box,fritz.box",
"0.debian.pool.ntp.org,time.fritz.box",
"1.android.pool.ntp.org,time.fritz.box",
"time.windows.com,time.fritz.box",
"time.nist.gov,time.fritz.box"
] ### CHANGED, default = []