You're right that the Canada thistles are difficult to get rid of. They are interconnected through the rhizomes underground. Your best bet for getting rid of them in an existing flower bed would be to spot treat with glyphosate (Roundup) by dabbing the glyphosate on the shoots of Canada thistle as they are actively growing, using a paint brush, or cotton glove over a rubber glove. Take caution to avoid dripping the glyphosate on your perennials because it can kill them, too if it comes in contact with them. However, the glyphosate won't be active in the soil, so as long as you touch only the thistles, your other plants won't be harmed.