Make a backup of the original demo templates

cp -rv /var/lib/ledgersmb/templates/demo /var/lib/ledgersmb/templates/template1

# on Ubuntu this was
sudo cp -rv /etc/ledgersmb/templates/demo /etc/ledgersmb/templates/template1

Go into the LedgerSMB admin control panel and change the template from demo to whatever you named the new directory.

cd /var/lib/ledgersmb/templates/template1
# on ubuntu it's in /etc/ledgersmb/templates
# backup your original files just in case
cp logo.png logo.png.orig
cp logo.eps logo.eps.orig

edit your new logo.png in Gimp to be something that you want e.g.

Save as logo.png
Also save as logo.eps

# copy new logo's into your custom templates directory
cp logo.png logo.eps /etc/ledgersmb/templates/template1/

Done