The TriMet red line is right outside the baggage claim at PDX.
http://trimet.org/
Take Amtrak from downtown Portland to Seattle.
You will have to rent a car for a day in Portland if you want to go out to see the Columbia Gorge and the waterfalls.
Be sure to visit Powell's Books in Portland.

If you book your hotel through Travel Portland , many of the hotel deals offer overnight parking and a breakfast without extra charge.

You can get around Portland for free within certain areas-

We have good public transportation in Seattle: http://metro.kingcounty.gov/

HTTY

PS You are better off without a car in Seattle.

Seattle has great public transpotation. Use the new-ish Light Rail system to get from/to SeaTac airport, then Metro bus to get around town. All of the usual tourist sights are easily accessible by foot, if you stay downtown (Seattle Center, Space Needle, Pike Place Public Market, the Waterfront, Pioneer Square historic district, etc.)

By November riding the buses in downtown Seattle will require payment, but certainly not as much as you'd spend on hotel parking charges. (They're currently free but that program ends by Oct. 1.) In November the weather will likely be lousy in both Portland and Seattle, so bring rain-friendly gear.

On arriving in Seattle on the train, I'd probably opt for a taxi to your hotel rather than using public transportation. The train station is not directly connected to the light rail or bus tunnel lines, and a cab will be very cheap from the station to any downtown hotel.

As for hotels, have a look at the Mayflower Park in Seattle. It's a lovely old hotel, usually quite reasonably priced, and very convenient to all the main downtown tourist attractions. A big plus is that it's adjacent to one of the light rail station entrances, so getting to the airport at the end of the trip would be a breeze.

Thanks everyone, I appreciate the info and tips!

On September 1 Portland is discontinuing the "free zone" within the city. Too bad, as it was nice to just hop on and off as needed without buying a ticket.

I just returned from a 8 day trip to both of these cities. We used the trains/buses in Portland - bought a $5 - all zones/all day ticket each day. We stayed downtown but used it to go outside of the free zones : Rose/Japanese Tea Gardens, to brunch and dinner (Tasty & Sons, Pok Pok) and to the airport. Transport was easy to use, reliable, clean. In Portland my favorite was the day trip to Columbia Gorge which needed a car - we started on Washington side, short hike, lunch, stops along the way, crossed over to Oregon, hatchery, short hike , Multnomah Falls. the Gardens (Japanese Tea/Chinese and Rose). I'd highly recommend it - you could rent a car from city and return the same day (no hotel parking) or do zipcar . We had a car in Seattle and could park free/overnight on street as we stayed in Capitol Hill but only used it for a day trip to San Juan Island via Anacortes. Otherwise we walked downtown (40 min) and cab'd it back up the hill There were buses but we wanted to walk to see the shops/restaurants. As a must see in Seattle I loved the Chihuly Exhibit in Seattle. We bought a combo ticket with the Space Needle. Chihuly allowed us to return the same day to view at night (have to get stamp before leaving). It was incredible by both day and night. All in all, we spent 1.5-2 days in each city so I think your time along with public transportation is a good one.