When we first did SE Alaska we got "chart portfolios", black and white photocopies of the official charts, at much lower cost than for individual charts. They're available from Bellingham Chart Printers, in full size or 2/3 size. A complete set for SE AK in 2/3 size cost about $500. Too bad they are not available for BC - had to buy those at list price, but they sure are nice to look at in color. For Puget Sound and the San Juans and Gulf Islands, you could go with the Region 15 Maptech ChartKit, a spiral bound book in color, about 1/2 half size.
We keep a very complete set of full-size paper charts for BC and SE AK, storing them folded generally in thirds in two very large zip-locs. To be able to find the one we want, we sorted them into an order that made sense to us (not by their chart number). Then we made Word documents that are tables of contents to the pile of charts in each ziploc. Could send you a copy if you'd like - send me your email. Now that we have very good electronic charts, we don't haul out the paper ones very often any more - but that may also have to do with the fact that space to spread out is limited on our small boat.
Along with Waggoner for BC, we like the Douglass "Exploring" series cruising guides for BC ands SE AK - some of the best info available on anchorages.