There are some important issues I'd like to raise:
1) The Holy Roman Empire extended beyond the borders of what currently are Germany and Austria. It included large parts of Eastern Europe. During the 18th century it also included the Austrian Netherlands (covering most of Belgium, Luxemburg and the south of the Netherlands). To the south, it extended into what is now northern Italy, Slovenia and Croatia.
2) Restricting the discussion to Kreuzer and Thaler implies limiting your focus to the Austrian/German heartland. The Speciesthaler/Reichsthaler has been legal tender throughout the Holy Roman Empire. Its name was Kronenthaler, known as Kroon/Couronne in the Austrian Netherlands and as Croccione in Northern Italy.
Domestically, Austria minted the Konventionthaler, divided into 120 Kreuzer. These Kreuzer only circulated locally. Whereas the Reichsthaler was the currency unit and unit of account, it was subdivided into different fractionals depending on the region.
3) I can depict only the situation in the Austrian Netherlands and hope for more input from the other regions outside the Austro-German heartland.
The currency system in the Austrian Netherlands was 'inherited' from what remained under Spanish rule. The prestigious high purity silver
ducaton continued to be minted till 1754 by Maria Theresia after which it was replaced by the Kronenthaler, also named Kroon (Dutch) or Couronne (French).
For trade purpose, there was the Albertusthaler, minted since 1612 also called
Patagon or Patacon. Its mintage was suspended after the Holy Roman Empire 'inherited' the Austrian Netherlands after the Spanish succession war.
Small silver and copper coinage remained in use. These were the silver 'escalin' (French) or 'schelling' (Dutch). The Patard (french) or Stuiver (Dutch) (Stiver in English) was still used but not minted any longer. Mintage continued in the Dutch Republic (northern Netherlands).
The copper Liard (French) or Oord (Dutch) continued to be minted and used for change.
Patard/Stuiver = 4 Liard/Oord.
Escalin/Schelling = 24 Liard/Oord.
216 Liard/Oord = 9 Escalin/Schelling = Kronenthaler/Kroon/Couronne
The former Patagon was equal to 8 Escalin and the Ducaton was equal to 10 Escalin.
4) About Thaler footage.
From the late 15th century and far into the 18th century, the unit of weight used to measure the silver against, has been the Cologne Mark, weighing 233.856 gram. (
http://en.wikipedia.org/wiki/Cologne_mark).
The official currency of the Holy Roman Empire was the Reichsthaler. Using a Cologne mark of silver, 9 Reichsthaler were minted. This was the 'Thaler footage'. During the 18th century, Austria minted the Konventionsthaler, with a Thaler footage of 10. Yet for use outside their homeland, the Kronenthaler, equivalent of the Reichsthaler, continued to be minted: from 1755 onward in the Austrian Netherlands and until 1801 in Lombardia (Milano mint). Emperor Joseph II met opposition against the introduction of the Kronenthaler minted for general use in Austria, since it was worth over 10% more than the Konventionsthaler and an odd number of 144 Kreuzer (rather than the 120 Kreuzer/thaler Austrians were used to). People were complaining about the strength of the currency.
With the rise of Napoleon, the Holy Roman Empire lost the Austrian Netherlands (1796) and Lombardia (1801) to France. Eventually the imperial crown was claimed by Prussia and in 1807, Franz II ceded the imperial crown. He then became the first emperor (Franz I) of the Austro-Hungarian empire. This also meant the final curtain for the Kronenthaler.
Instead, Prussia started minting smaller Thaler, using a 14 Thaler footage. The Prussian Thaler contained 16.704 grams of fine silver. Germany was not united, but Princes and Dukes ruled their own region and minted their own Thaler until far into the 19th century. Some differences in weight and fineness arose. The success of the Thaler hence also was the reason for its replacement by the Mark. In the Austro-Hungarian empire, the (10 footage) Thaler was replaced by the Gulden, which was decimalized to 100 new Kreuzer in 1857.