To enter a Lat/Lon waypoint in a route in ForeFlight on the web, enter it in the form: 4015N10658W
Currently, Latitudes must be 4 digits in the form DDdd and Latitudes must be 5 digits in the form DDDdd. If the Longitude is less than 100 then enter a leading zero eg: 4253N08549W
Additionally if you already have a route planned, you can 'rubber band' to a specific lat/lon by clicking on a point on a route leg and then drag it to the desired lat/lon location.
Also if you locate the position on the map, you can right click on the map and select the Lat/Long value for that location to add it to your route.