Won't look pretty on the input screen but, if you must, adjust the In-state municipal bonds based on the ratio you want.
For example, out of $2,500 of muni bonds interest, $1,000 is in-state. That means 60% would be taxable to the resident state. Let's say the premium is $625. That would result in tax exempt interest of $1,875 ($2,500 - $625). Lacerte will take 60% of $1,875 (i.e. $1,125) as taxable income on the state return.
If you say that's not right because the premium for the in-state amount should really be $312.50 instead of $250 ($625 x 40%), you'll need to plug in a make-believe in-state muni bonds amount to yield the result you want. In this case, you want the state taxable amount to be $1,187.50 (i.e. $1,875 - ($1,000 - $312.50)). Since $1,187.50 is 63.33% of $1,875, you'd need to plug in $917 ($2,500 x (1 - $1,187.50 / $1,875)) on the line for In-state municipal bonds.
Lacerte will then compute the out-of-state taxable amount based on ($2,500 - $625) x (1 - $917 / $2,500) and yield $1,187.