I've been known to permatex a few things in my days..however if there is a gasket made that should be the first go-to. Make sure both srufaces are clean, clean, clean. No residue from old gaskets. Like mentioned, if there is a rubber seal-gasket interface I like to use a small bead of permatex to seal between and around the rubber seal.
If the mating surfaces are skewed ever so slightly I have used a coat of the proper goo on the gasket. I will lay a small bead, spread it with a small putty knife and assemble it that way.
Another common mis-step is proper assembly with the gasket. Make sure you tighten the bolts evenly.
While the silicone may be a good band aide I don't like using it exclusively on fluid containing cases/reservoirs as the actualy layer created can be quite thin and not very stong under pressure or certain solutions.
You can even get a sheet of comparable gasket material from the auto shop and using the old gasket (if intact) a pencil and a hobby knife you can make a new gasket rather easily.
2001 #62. Ohlins rear/valves, Micron high mount, HyperPro damper, SharkSkinz, Tyga billet triple clamp, Tyga Carbon Fiber fender and hugger, Ti bolt/custom subframe/alien motion 8 cell diet, 15/41 520, COP conv. PCIII, Venhill lines, modified air box, turn signals in headlights...<deep breath> ZG Touring windscreen, Tech G rear sets, CRF450 rear master w/HRC cover, Tokico 6 pots w/V-pads, CRG Bar end mirrors, PSR Shorty levers-use only clutch, wanna-be basic racer paint, Roman Gold PC wheels