Hi, Emily. The way you get the discount when you purchase tickets online is to click the link near the bottom of the ticket search window that says "further search options" or "weitere Suchoptionen". This takes you to a pop-up window that has further filter options. In the middle of that window is a drop-down box in which you choose what kind of BahnCard you have: none, BahnCard 25 2nd class, BahnCard 25 1st class, etc. This will adjust the price that is displayed and charged.
Also, you can load your BahnCard into your Bahn online account along with your Handy-tickets so you don't have to have the physical card with you, or as a backup if it's lost or stolen. Instructions are on the site under BahnCard tab.
Since you've used a BahnCard before, I assume you know it's an automatically renewing subscription. You have to send your cancellation notice to arrive six weeks before the card expires, or it just renews and charges your card. I sent my cancellation the day I received my 3-month BahnCard and it worked perfectly. The card was valid for the full time and then cancelled itself with no issues.
Hope this helps. I'd paste in screeen shots but it won't let me.