I don't think it's a daft question at all, Order in the border - I have been musing over mulching myself recently! the thing is, all the advice in books etc seems to assume that you have a totally empty border, where everything dies down (at the same time) for a good old Autumn clear up and there is lots of bare soil. It probably assumes that people grow a lot of summer bedding and vegetables.
In practice, I have found that that is rarely the case in my garden - I only have a tiny veg plot, and in my borders at the moment cyclamen are popping up, fuchsias are still flowering, lots of my perennials are still in growth - if slowing down a bit - and by the time they disappear underground for a rest, I find that my hellebores and early spring bulbs are starting to stick their noses out. In spring everything seems to get going very quickly, so there never seems to be a perfect time to mulch everything.
I tend to agree with Verdun and prefer mulching "as I go" when planting, or when something has died back a bit leaving some bare soil. However, I have lots of leaf mould and compost now, having just emptied out the cooked stuff, and I don't have space to store it. A week or so ago, I spread some of that about amongst the plants as best I could - but I forgot about the cyclamens, which sit very near the surface. They seem to be finding their way through though (I have spent a lot of time peering at the soil, to the consternation of my neighbours no doubt!). I spread about 2" of mulch in between plants. The rain tends to even it out and flatten it. At this time of year, the worms are very active and it gets taken down into the soil very quickly. In the spring, I will mulch again, adding some bonemeal to the compost - again, it's difficult to get the timing right in spring as the soil needs to be moist and if we have a dry spell that can delay my mulch and the plants are already in growth.
As FB says best to avoid smothering the crowns of perennials if you can, and I make sure that any mulch is not in contact with woody stems of shrubs as it can rot them.
I have also been wondering whether mulching will affect my recent application of nematodes (against slugs and vine weevil). From the amount of slugs I have seen whilst clearing up leaves, maybe it has.