Both solution are OK.
All depends the kind of statistic that you want on google and how you want to group them.
The syntax is the domain or subdomain = the google ID
If you are on the site
www.domain1.com and that you have setup a google list with only subdomain1=XXX then you will NOT have any code generated as you will not have any exact match between the domain and the list (here subdomain).
So you have to provide exact match on what you want to provide.
As I don't know how you have grouped the slave site in a give Site ID then I can not replied to you the method that you have to choose.
If you have a
Site ID = Slave1
Domain =
www.domain1.com
subdomain1.domain.com
Then you have to setup a Google Analytic in the Slave1 website corresponding to the
ww.domain1.com=Google ID 1
subdomain1.domain.com=Google ID 2
or if you want to have a single statistic use both Google ID 1