If you can't resolve
the "partial pages getting lost in the printer" issue, you can try to use form leaders to feed your printer with a
proper 8.5x11" sheet while printing a partial 1- or 2-checks page in
normal portrait orientation.See https://intuitmarket.intuit.com/fsg/businesschecks/formleaders.aspx
for an example of form leaders. Check your local office supply store, search on
the Internet or order from Intuit.
I use Voucher Checks (1 business size check + 2 stubs on an 8.5x11"
sheet). My printers do not have a manual feed tray or 2nd paper tray that can
easily be reconfigured to feed partial pages (1 or 2 checks left from a
3-checks-per-page sheet), so for my occasional check printing needs Voucher
Checks are easiest to use.
When making a purchase decision for a new supply of check forms and considering
your own check stock to use, consider how easy or difficult it is to feed special
forms or odd-size partial pages into your printer.