I agree with Balaji -- I think this is the most straightforward way to interpret the SWAT output for sediment.
-- I typically try to calibrate on monthly loads rather than concentrations, if only because grab-sample concentrations can be so variable. On the other hand, it's good to remember that "observed loads" themselves are rather uncertain numbers based on observed flows (fairly reliable) and observed concentrations (potentially highly variable).
-- There is some question in my mind whether the MUSLE results include all grain sizes or just the suspended fraction. The USLE results should include all fractions because this equation was based on plot-scale studies where all grain sizes were captured. But MUSLE was based on (if I recall) small watershed-scale loads for 18 watersheds from the southern USA, and I don't know if bedload was included or not -- and if so, whether it could be partitioned between field and bank sources. MUSLE loads are almost always less than USLE loads, and I've presumed part of this was because of missing the bedload component, along with other sediment traps along the way between fields and the gauging station.
-- I presume if you use the default sediment equation in SWAT, which assumes silt-sized particles, and you calibrate to the suspended load, then you simply can't say much (if anything) about bedload. If you use one of the grain-sized specific methods, then make sure you calibrate only the clay+silt fractions to the observed TSS, as Balaji points out.
-- Our measurements of TSS involve filtration of a known volume of water through pre-weighed glass-fiber filters, which are then dried at 105 C and re-weighed. The dissolved mineral component is thus not included (except for just the bit of water that wets the grains on the filter, after filtration). TSS includes both inorganic particles (usually dominant in agricultural rivers) and organic particles (volatile suspended solids (VSS), which are often algal bodies that can dominate in the outflow from reservoirs and lakes). If you're most interested in soil erosion of largely inorganic soil (>95%), you probably should subtract out (most of) the VSS if you know it, although I don't know of many who do this.
-- I will add that in recent calibrations I've been working on in systems with many lakes, the model results are very sensitive to the grain size (D50) I set for each lake, along with NSED values. The lake D50s had to be set in the fine-silt/clay range for the lake to pass much sediment downstream. And, NSEDs had to be set low, in the 1 mg/L or less range -- if they're too high, then lakes become sources rather than sinks of sediment, which is not likely to be realistic in most cases.
-- If your modeled loads are too large, then SWAT is either generating too much sediment in the HRUs (reduce erosivity, slopes, CNs, or increase vegetation cover somehow), or there are sediment traps along the way (Ponds, Wetlands, Reservoirs) that are not being accounted for.
-- And, be on guard that the channel erosion equations are not unrealistically eroding sediment from the reaches. You should check to see where all your excess sediment is coming from. I think SWAT-CHECK will tell if if it's field or bank erosion. Once you know the source, you can then target the proper parameters in SWAT to tone down the modeled loads.
Best of luck,
-- Jim