Doug You mentioned that there are a few places to stay close to the bus/amtrak station. Can you tell me the name of the places that you were speaking off?
There are several on Marine Drive, which is the street that runs along the bay. The best way to find the location and prices might be to look at Booking. com
http://www.booking.com/ We have used them a lot, and they have good prices. However, all motels in a city may not be listed.
We stayed at the Rose River Inn (1510 Franklin 1-888-876-0028) at the start of a trip a couple of years ago. It is a nice B&B and the folks are "bike friendly", but it is uphill from the bus station.
We have also stayed at the Best Western, Lincoln Inn. It is located all the way across town, almost on the approach to the bridge to Warrenton. Another, the Columbia Inn is a little more down scale, but perfectly adequate and clean. It seems like it was just a few blocks from the bus station.
If you can put your bike in running order at the station, you can get to all of the major motels in town within 15 minutes.