Well the properties are set in the backoffice (just like documenttypes), but in code you can do this.

You first need to get the alias of the field, if you're using modelsbuilder you can do it like this:

var customMemberProperty = Member.GetModelPropertyType(_publishedSnapshotAccessor, x => x.CustomMemberProperty).Alias;

or just use the string alias of the field, in this case "customMemberProperty".

Then get the member by various means (email or id for example)

var memberToUpdate = _memberService.GetByEmail(emailAddress);

Then update the values:

memberToUpdate.SetValue(customMemberProperty, "NewValue");

And save them

_memberService.Save(memberToUpdate);

Done!