In general, it's best to work with templates as much as possible.

Remember that you can make use of macros and define them on template and on host level. So when you create an item in your template, make use of macros as much as possible. This way when you have an item in your template that doesn't work for one of your servers, you don't have to create a second item. Instead, you could just alter the macro on host level.

Zabbix provides a set of standard templates that are too aggressive in my opinion. I suggest that you create your own templates or strip the original ones and only keep what you really need to monitor. Only check items every x number of minutes, instead of seconds, and keep the time interval for history as short as possible. Mostly, there is no need to keep all data for months and for reference most of the time, trends will do just fine.

Often,when I install Zabbix for a customer, I create a new group for the templates that I will use and keep the original Zabbix templates in the template group as reference for later.

Avoid the creation of items directly on hosts. Remember the previous point where I have mentioned making use of macros on template and host.

It's easier to maintain your users when you connect Zabbix to your LDAP or AD.

Remember that permissions are based on the groups and not on user level. Try to make use of groups as much as possible as it's easy to enable / disable them.