You're tackling the weeds the right way. If you pull them, try to make sure you get the whole root out. If you spray with Roundup, use some kind of shield or barrier to protect your perennials from drift or overspray. Wet down the weed foliage, but make sure you don't get any on your good plants. (If you do accidentally hit a perennial, rinse the Roundup off with water immediately.) For it to work best, you want the Roundup to stay on the weeds for at least two days before being washed off by rainfall. It's pretty common to face a fierce weed battle in a new garden. Once you get it under control, their reduced population means fewer weed seeds to contend with and the maintenance will be considerably easier. A 3- to 4-inch layer or organic mulch like shredded cedar will also help.