I like the idea of the different levels which gives you a lot more scope and interst as far as planting goes.
I have been establishing a (much smaller) garden from scratch over the past six years and like you I am gardening on heavy clay. It will probably make life easier for you if you add plenty of "organic matter" to the clay - sounds hackneyed I know but it does make managing your soil a lot easier even if you let it break down on the surface and let the worms and bacteria do the hard work. Scrounging other peoples lawn mowings and hedge trimmings for mulch is a dodge I have used in the past. Sounds wierd but it works! You may not have time to do it anyway with all your other projects and the soil has often been too wet to dig effectively this year anyway.
I like the idea of bulbs which was suggested earlier and you may find that the supermarkets are starting to sell these of at a discount at this time of year. With a bit of planning it should be possible to have a succession of flowers throughout the year. A layer of sharp sand or grit in the planting hole helps stop them rotting and discourages slugs and snails. Lower growing bulbs would be ideal for the containers you mentioned and these can be planted in layers if you wish with the taller varieties at the lower level.
The idea of shrubs is a good one too. I especially like hebes and there is a great variety of different foliage colours and sizes. They are very hardy and have the additional advantage of rooting easily from cuttings so that you can easily get more plants or replacements as needed or for exchanging with other gardeners. Open compost and a plastic bag to cover the cuttings is all you need. Same applies to Euonymous shrubs and variegated or even common Holly, which will provide some Winter interest when nothing else is growing and are all low maintenance.
You could brighten up the dark wall with some ivies - again there are some colourful varieties which can be propogated from cuttings easily and are evergreen and thrive even in shade. An occasional trim keeps them in check so that they don,t swamp the rest of the garden. They can look decorative grown on branches as supports or even wire frames as topiary - quite easy to do. As far as the timber itself goes, if you are undecided about colours a possible compromise might be linseed oil. It gives a durable coating and mellows with age without getting too dark and might blend in quite well.
You could think about a cammomile lawn which has the advantage of being fragrant and standing up well to foot traffic. Some people plant the cammomile through a weed suppressing fabric which reduces the need for weeding whilst the plants get established and you can either raise your plants from seed or buy them as plants.
I have got a bit carried away with comments here so it's time to give over now! I hope there is at least something here of use to you.
Enjoy your garden anyway,