Hi Tina,
There are top down tools like the PDT and the old excel spreadsheet tool BP used to used (no longer on portal, might have used it at Ascension in the early days?)
However those kind of tools are very much top down exploration, a bottom up approach by experienced people in your team is needed to get the accuracy needed for quotes. If you search for 'IPA or initial process assessment' and 'application assessment' on the portal you will find how we used to do it (hopefull those documents are still on the portal, they have had a habit of removing useful stuff in recent years).
Finally, for fixed price work add a contingency (especially for process areas or customers you know tend to be difficult) plus a project management premium.
Also, the biggest reason for projects going past estimates is poor management of change. Pin you internal client to the PDD definition, changes from that need to go through a change board process because they cost. If you are having problems in the PDD definition phase it might be worth looking at how it is done. Remote definition work is extreamly difficult, better to sit with the team working the process for a couple of days watching all the scenarios or use a process discovery tool like timeline or celonis.
