Troy,
Welcome to FretlessBass.com
I think that you made a good buying decision in the bass you have now. Many of us prefer the unlined fingerboard, I would avoid marking the fingerboard until you have spent a bit more time on it.
The best lesson I ever learned from my Dad was this, he said "Son, there's a technique to everything." You need to get your left hand technique down.
First I would find a local bass teacher who actually plays fretless. If one is not available then consider an upright bass teacher but let him/her know that you want to learn intonation (left hand technique) on the electric fretless.
What you need is to get the proper left hand positioning down cold. Practice scales until you are an expert.
I think that the fretless player needs to involve all of the left hand fingers in order to achieve good intonation. If one does not cultivate a position referenced left hand technique then it is more difficult.
So exactly what technique am I referring too? Well, there are several, depending on what scale form you are playing. For starters play a F major scale in the 1st position.
This major scale should have the familiar Do Re Mi Fa Sol La Ti Do sound.
In the following, an Open string is called the zero (0) position and the 1st position is equivalent to the 1st fret, etc. So the 7th position on the D string is an A note, equivalent to the 7th fret on that string.
F 1st position E string 1st finger
G 3rd position E string 4th finger
A Open
Bb 1st position A string 1st finger
C 3rd position A string 4th finger
D Open
E 2nd position D string 3rd finger (2nd finger also OK)
F 3rd position D string 4th finger
This is real easy and a good place to start. Play it ascending, then return to the lowest note the same way you came up. Not all scales are symmetrical ascending and descending. For now assume that they are.
Now move the scale up two semi tones and play a G major scale. This is G major from the 3rd position. This key has one sharp F#.
G 3rd position E string 2nd finger
A 4th position E string 4th finger
B 2nd position A string 1st finger
C 3rd position A string 2nd finger
D 5th position A string 4th finger
E 2nd position D string 1st finger
F# 4th position D string 3rd finger *this is the dumb finger and may need more work.
G 5th position D string 4th finger
Play this scale ascending and descending. You will probably feel some stretching in your left hand, this is normal, just don't over do it and injure yourself. Take a break if your hand/wrist heat up.
VERY IMPORTANT: When playing this type of scale, the left thumb should be placed opposite the 2nd finger, or root note, and stay there until you need to move to another position. Consistent thumb position is the vital key to good intonation on fretless. When one changes position the thumb position also changes and you MUST make your thumb movement crisp and precise. This means that you need to know where you are going and plant your thumb correctly BEFORE or simultaneously to playing the intended note.
This G major scale from 3rd position is what is called a movable scale, you can move it up or down the fingerboard as needed. Try playing the same scale in various keys. It should get physically easyer as you move up the fingerboard.
Take a look at this thread:
http://fretlessbass.com/viewtopic.php?t=99
Looking forward to learning if this advice is helpful. Please check back in soon.