In a traditional lime lager, zest the limes by hand and then juice them into a large stainless pot. Hand zesting is preferable, to limit the amount of bitter pith that is included in the mix. Heat the zest and juice together, to a minimum of 165°F, for at least 5 minutes. This will pasteurize the mix, eliminating microbial concerns, but it will also help express some essential oils from the zest. Using a nylon mesh bag will allow for separating the solid particulates, leaving a nice clean juice to work with. Cornelius kegs are a common item around the brewery, and they work great for preserving homemade extracts and juices. Since they do not allow light penetration, UV degradation is reduced to minimal levels, and purging with co2 will prevent advanced oxidation. From these kegs it is possible to dispense the proper amount of favor, whether it be for a single glass, or a whole vessel. If larger quantities are in order, use a dedicated pressure vessel, sized appropriately (a second fermenter).
Some ingredients are much more difficult to process than fruit juices. Juniper berries, licorice root, orange peel, or heather tips are just a few that can clog up pipework or float on top of your brew. Using a mesh bag in the kettle is a great idea, but you may need to weigh down the bags to keep them submerged during boil. An alternative way to approach these items is to make an extract from them, and add the extraction back to the brew. Licorice root is a pronounced flavor, and it can be quite polarizing. If you are looking to balance complexity with approachability, then an extracted titration may be just the ticket.