This is where the fundementals of navigation come handy...

You can use pilotage, dead reckoning, your nav radios, a clock, and a compass to navigate. But also, planning your checkpoints carefully using landmarks and VOR/NDB stations will help you. Otherwise, a waypoint such as an airway intersection is more difficult to navigate to without a GPS. It can be done, but you have to be a competent navigator.

At the top of the flightschool board, is a sticky named Sim Flight Training series. I would highly suggest reading through the series, especially part 5 and part 5.1 which discuss VOR and NDB navigation.

I would also suggest heading to your local General Aviation airfield and getting some old aeronautical charts. These will help

I think learming how to use the nav radio feature was one of the great things about fsx. Flying to ndb's or vor's makes it a lot more interesting.  Give it a try.

The simplest way, assuming you are flying in visual conditions (I hope so, in a Cub) is to select visual waypoints. You can see them coming.  

But if you're looking to predict how long it will take you to get from A to B, using only the tools available in the sim, you need to first create a flight plan, then pull up the Nav Log, which will give you time estimates based on the distances vs. your aircraft's known airspeed.

I don't use that function much, so I can't remember if it factors in wind or not (probably not, unless maybe if you set up the plan after actually starting up the flight while on the ground at your departure point).

So... assuming you don't have an estimate based on the effects of wind... what you do is note the time passed on the first leg, and adjust the estimates for the remaining legs accordingly. If you are changing course from point to point, the wind's effect will be different, but... just knowing roughly what direction the wind is blowing from makes a big difference.

Ultimately, to really do it right without a GPS, it's best to have a chart, a plotter,and a flight computer. Expired charts can be obtained for free
at any FBO, and while you're there you can buy a small plotter and "whiz wheel"-type flight computer for less than $20.

In real life, I've never navigated with GPS, and often without any radio navaids at all. I rarely pull out the whiz wheel or plotter in flight, but I've always done fine by making a good nav log beforehand, using the chart, plotter and computer, and "plugging in" recent weather reports and forecasts,  then carefully noting my arrival times at each waypoint to constantly update my actual groundspeed. This allows me make pretty accurate estimates of when I will arrive at the next waypoint. And as I mentioned earlier, a critical part of VFR navigation is to select good visual waypoints.  

In the long run, especially flying a Cub or similar, you can afford to be a few minutes off in your estimates, as long as you make your guesses conservative, so you don't risk running out of fuel enroute, or worse yet, when you're down low looking to make an approach.