so I inputted the chords and chose real tracks from the list for piano and bass, but when I hit play the thing was a nightmare.
In addition to selecting the proper RealTrack (3/4 versus 4/4), it also makes me wonder if you put the chords in the correct position for the song. Each bar in BIAB contains two cells and each cell can contain two chords. To enter the two chords in a cell, just separate them with a comma. Move on to the next cell and do the same thing. The first cell in each bar (in general) represents beats 1 and two; the second cell in each bar represents beats 3 and 4 (for a 4/4 song).
To enter a chord in just the 2nd half of the cell, just type a comma followed by the chord.
Also, there is always a default style loaded when you started BIAB (which you can change), which will play in addition to any instruments you substituted. So if you only substituted the bass and piano, whatever instruments defined in the underlying style for drums, guitar, and strings will also play. If the underlying style is a 4/4 straight feel and the piano and bass you selected were a swing feel, it just isn't going to sound very good.
What BIAB plays is all based on styles, with substitutions allowed. Unless muted, however, all instruments defined in the style will play.
My suggestion is to decide the feel of the song you want to use (4/4, straight or swing, 8th or 16th feel - you usually use 8th feel for faster tempos and 16th feel for slower tempos, but it depends on the song).
Frame out your song using the three numbered boxed on the main screen. The first is the bar number the song starts on (to take into account an intro), the second number is the number of bars in the song, and the third number is the number of times to repeat the song (between the start number and the end based on number of bars). By default, BIAB will add a two-bar ending to the song after the last chorus plays.
Once you have framed out your song, enter the chords in the appropriate bars (I'm not getting into advanced features here, so I'm just assuming each bar starts on a beat).
Set an appropriate tempo, and then go to StylePicker to choose an appropriate style based on everything discussed above.
Now hit play/generate to listen to the song. It won't sound like the original, because of the style you chose, but the chords should line up on the right beats and everything should play in the same feel.
Once you're okay with this, now you can start looking at substituting styles and/or individual tracks. If you substitute tracks, make sure (at least while you are still learning) the style has the same attributes as the underlying style. RealTracks can be soloist tracks (like a guitar lead) or rhythm tracks, and will indicate that in their name. You'll also see if they are 4/4 or 3/4 (waltz styles as well). The RealTrack picker will also show appropriate tempos for the style.
Hopefully this will get you closer to what you want to do. It takes longer to read this post than to actually do everything described.