| I play both Electric and Upright and was fortunate enough to learn both about the same time. Although, like most bass players, my first instrument was guitar (then again, when your 6, most people don't want to play bass).
Since you are coming from the upright world, using the 3rd finger to fret notes is going to feel odd, and that is ok, there is nothing wrong with that. Even electric bass players go by that rule but they don't associate it with an "Upright" technique... ie... 1st finger 1st Fret, 2nd finger 2nd Fret, 4th finger 3rd fret... This will work out just fine until you start working your way up the neck, you will start to feel cramped playing that way.
Start with your 1st finger on the 5th fret, and use 1 finger per fret. At this position, you should not feel any uncomfortable stretching required to reach all 4 frets. Just practice playing 1, 2, 3, 4, finger patters (1, 3, 2, 4,... 1, 4, 2, 3, etc etc) to get your self used to using your left hand and all 4 fingers.
With your right hand, you want your hand to be in the position of holding a small tennis ball. (if you ever took piano lessons, similar to that). use your thumb to mute the B string and E string (rest your thumb between them and move it away when you need to use the B / E strings)... without even playing any left hand notes, practice softly playing / alternating fingers (pointer, middle)... do this softly until you are used to it.. practice raking pointer finger on the G to D string, and then middle from G to D...
If you find yourself playing too hard all the time, you could look into building a "Ramp" to force yourself from digging in to much (this will be the same effect of playing above the fingerboard.
Hope those pointers help you out a little bit?!
The rest is relating the note positions to the side markers... Piece of cake once you get the hang of it. | 
