If you're using M&S to develop your cost estimates, you need to understand a couple things about the base costs they use. Those costs represent the national average based on the data they've collected. Those base costs include some things and exclude other things at the various quality levels. Your first step is to select the appropriate base cost using the description for the category that best fits your subject. Make adjustments to that base cost to account for extras or any items your subject may be lacking but that would normally be included in that base cost. That includes adding for A/C or deducting for a lower quality roof, depending on what your subject has. Gotta add for flooring, fireplaces, extra insulation, etc.. After you have made whatever modifications are appropriate to the base cost to reflect the features your subject has, then the multipliers come into play.
There are multiplers for size and shape to reflect the economy of scale that affects costs, and there are multipliers for wall height (taller ceiling heights cost more to build and vice versa). These multipliers are applied to the base cost.
The last multipliers are for location and time. The base costs are published once a year,and then quarterly multipliers are issued every quarter to update those costs as of that quarter. The location multiplier is used because costs vary by locale. For instance, I did a Cost Approach today on an office building and ended up using a 1.10 for my location, meaning it costs 10% above the national average, and a 1.04 for my quarterly multiplier, so my composite rate was 1.144. This location/quarterly multiplier is applied to my cost new after accounting for the base costs, adjustments to the base costs, and because I'm working out of the commercial cost guide, separate line items for indirect expenses and developer profit. The residential book uses base costs that include most of those items, which is why base costs for constyruction are commonly going to exceed $95 or $100 a foot for "Average" quality construction after it's all said and done.
So to recap, you adjust your bases costs for features, then again for variances in wall height, shape and size. Then you apply the quarterly multiplier and the location multiplier to modify your subtotals of all improvements for the area the subject is located in and the time period during the year since that base cost was last published.
As others have noted, sometimes the bases costs and time/location multipliers M&S uses lags a bit, sometimes by as much as 6 months. This is why it's a good idea to constantly calibrate your costs estimates by comparing them to current construction contracts whenever you can. Trust, but verify, if you know what I mean.